115-Understanding Tomato Diseases and How to Deal With Them

| Care, Podcast

Tomatoes are one of the most popular garden edibles. Unfortunately, they are also one of the most challenging. Highly disease-prone, tomato plants often start strong and set a tantalizing crop of fruit only to transform into a living laboratory for pathogens – practically overnight. This season, I’m growing 43 tomato plants of differing varieties – mostly heirloom. In spite of my diligent proactive measures, I still wage war with tomato diseases every year. We all do, but hopefully, you haven’t let it get you down.

Disease does not mean we have failed. It’s just one more opportunity to learn, and there are always new developments for management, which is why I asked Dr. Meg McGrath to join me for today’s episode.


Dr. Meg McGrath

The focus of much of Meg’s work is in helping farmers prevent, identify and manage disease in their larger-scale operations, but she also keeps busy managing her own massive tomato plants in her Long Island-area garden. (photo: Courtesy Dr. Meg McGrath)


Meg, who started gardening nearly 40 years ago, is an Applied Plant Pathologist and Associate Professor from Cornell University’s School of Integrated Plant Science. Her areas of expertise include organic disease management, vegetable diseases, epidemiology, and fungicide resistance. In other words, we couldn’t ask for a better guide to walk us through the ins and outs of tomato disease management and prevention.

Meg jokes that disease pathogens enjoy tomatoes as much as we do. Yet – even though tomatoes are highly susceptible to a wide range of fungal, bacterial and viral diseases; you can tip the scales a bit in your favor by following good proactive practices.

Proactive Disease Management

Have you heard of the disease triangle? It represents the three elements which must be in place before a disease becomes active: a host, a pathogen and the right conditions. Remove any one of those three elements, and disease won’t affect the plants in your garden. Period. Sounds easy, right. Well, it’s not, but many of the preventative measures are.

The first and best thing you can do is to keep as many diseases out of your garden as possible, and that starts with plant selection.

Never buy a seedling that shows any sign of disease – like withering, misshapen growth, dark or yellowing spots, or discolored foliage. The lowest set of leaves may have naturally reached the end of their lifecycle and turned pale or yellow, but other yellowing is a red flag.

That said, most diseases won’t rear their ugly head until the plant is more mature, so buy seedlings from a trusted supplier. The same is true of seeds. There are plenty of sub-par seeds available on the internet, but those put you at greater risk of bringing seed-borne disease into your garden.

Buy seeds from reliable companies. It’s not a guarantee that the seeds will be disease free. It’s impossible to visually determine if a seed infected, but you can be confident that quality suppliers have taken necessary precautions. So, the risk is much lower.


Septoria Leaf Spot disease

Septoria Leaf Spot is a common fungal disease in the home garden and one of the most destructive to tomato plants. (photo: Dr. Meg McGrath)


Look for disease-resistant tomato varieties. If your area is prone to a certain disease, remove the “host” aspect of the disease triangle by avoiding the plants most vulnerable to that disease. Your local County Extension office and Master Gardener programs are both good resources to identify which diseases you should be most concerned about.

There are some good options on the market which are inherently resistant to some of the most common tomato diseases. The plant tag or seed catalog descriptor will indicate with markers like F (resistant to Fusarium Wilt) or V (resistant to Verticillium wilt).

Resistance doesn’t mean bullet-proof. It just means those plants will put up a stronger fight against that type of pathogen.

While some diseases are transmitted through the seed; they are more commonly transmitted through the air, from the soil on water droplets, or by insects.

Bacterial diseases must penetrate the surface of the plant through a cut, a wound or some natural opening. Pathogens are tiny, so they only require a very small opening. In fact, even a broken tomato hair creates an opportunity.

Does that seem discouraging? Take heart. Bacterial diseases are not the most common enemy.

Viral diseases are also less common, but those are the real killers. They attack the entire plant system. You can’t remove a stem or two affected by viral disease. Once it’s in the plant, that plant has to go. More on that in a minute.

Fungal diseases are the most common. Fortunately, they are also the easiest to treat. These pathogens affect the plant from the its surface, and they grow when the foliage is moist – from rain, irrigation or humidity.

In fact, how I irrigate my garden has a lot to do with my ability to prevent, or at least reduce the moisture-related diseases that are common. For me, it’s drip irrigation whenever possible to keep water off the foliage and direct it efficiently into the soil for ready access by the plant roots.

Once you get your tomatoes into the garden, put down a 2-4” layer of mulch over exposed soil around the plants. That proactive step will create a barrier against soil-borne fungal pathogens which could otherwise splash up onto foliage during rain or when you water.

Mulching doesn’t mean your plants will be disease free. Disease prevention is a little like building a fence. Buying wisely and adding a layer of mulch will block two points of disease infiltration, but you need to really circle the wagons with other proactive steps – like irrigating properly.

Whenever possible, water at the base of the plant. I’ve used Rain Bird drip irrigation products for years, because I know that their drip irrigation products keep moisture off the foliage. Of course, rain is inevitable, and I live in the humid southeastern U.S. So, I know there will be no shortage of the moisture fungal pathogens need to reproduce, but I’m reducing those opportunities when I avoid overhead watering.


aphids on tomato foliage

Some diseases can be moved from plant to plant by insects. Aphids have a well-deserved reputation for being transmitters of disease.


Are you a smoker? Tobacco products are often tainted with Tobacco Mosaic Virus. All it takes is for you or a tobacco-using visitor to make contact with a tomato leaf after handling a tobacco product, and you might soon have to remove a virally-infected plant. So if you smoke or chew, be sure to wash your hands thoroughly or wear gloves before handling tomato foliage.

Proper support is another worthwhile disease prevention step. When the plant is kept up off the ground, soil-borne disease has much less opportunity to make contact with foliage. Good air circulation also reduces infection from fungal disease. Although the fungi may blow onto foliage, the continual movement of air can prevent it from growing.

A well-supported plant will also be easier to monitor for signs of disease, so you can get a jump on removal when necessary. That’s a very good thing, because in spite of all these proactive steps, disease will take hold.

The Tomato Disease Cometh

I circle those wagons every single year, but I still see some of my tomato plants struck with disease each summer. So will you. When it does, there is still hope, but you need to act as quickly as possible.

As soon as your tomato plants show signs of fungal or bacterial disease – such as yellowing or black spots on foliage – cut the symptomatic stems out. You need to remove more than just the affected leaves, because odds are good that the entire stem has been infected.

Unfortunately, odds are also pretty good that other foliage in the area will have already been infected. Wind-borne pathogens move quickly through a garden, and water-borne diseases really get around during periods of heavy rain. Typically, plant foliage won’t show symptoms of disease until a week after infection occurs.

Managing the spread of fungal spores, is a little like controlling water during a flood. You can slow it down, but it just keeps coming.


Powdery Mildew disease

It’s easy to spot the tell-tale white spores of Powdery Mildew, but fortunately, this common fungal disease is also one of the easiest to treat. (photo: Dr. Meg McGrath)


This is why – once disease has struck – the rest of the season becomes a race to the finish. From that point forward, you will be removing symptomatic plant stems through the rest of the growing period. Meanwhile, the remaining asymptomatic foliage can continue to photosynthesize, so the plant will be able to produce and ripen fruit.

The point of removal isn’t to cure the plant – it’s to remove as many pathogens from the area as possible. Removal also reduces the risk that the pathogen will be transferred by an insect.

This year, I’ve spent 2-3 hours every couple of days removing stems of leaves showing signs of disease. Bear in mind, I’m growing 43 plants this year, so your disease management time will probably be a lot less. Truth be told, many of my plants look pretty naked in August each year, but I’m still harvesting fresh tomatoes thanks to a few “healthy” branches at the top canopy.


Sungold tomato stripped of diseased foliage

Living in the humid Atlanta-area means that disease is a fact of life at some point for me every season. As the summer wanes on and I remove affected foliage, my tomato plants start to look very bare. What you can’t see in this picture is the remaining green foliage at the top of this plant which allow photosynthesis to continue, so these tomatoes can ripen.


Now if your plant is attacked by a viral disease. Don’t just cut out foliage – cut your losses. The entire plant needs to be removed completely, before the pathogen has the opportunity to spread to other plants.

Aphids and thrips are notorious for moving virus from one infected plant to another. They feed on an infected plant and, when they move and suck the juices from a healthy plant, the virus is transmitted through their proboscis (sucking mouth part).

Whether you are removing foliage or the plant itself, never add diseased plant material to your compost pile. Many pathogens survive typical backyard compost temperatures as well as frigid winter weather. In other words, the pathogen is likely to remain in the compost you spread in your garden and – even after months of freezing temperatures – will be lurking to strike again.

Meg also recommends that you “leave no tomato behind”. If you spot a damaged tomato while harvesting, don’t let it hang on the vine, and don’t add that to your compost pile either. Just like foliage, a tomato fruit can transmit pathogens, so don’t leave any on your property. If you don’t eat them, throw them out.

Here’s something that might surprise you: Bacteria pathogens are able to overwinter on your tomato support. If you use wooden stakes or any porous material, bacteria can gather on the surface (forming what’s called a biofilm). Then after you stake plants the following spring and once conditions are conducive, the bacteria will infect susceptible plants.

Metal support – like my Ultimate Tomato Cage is a better choice for a disease-prone garden. There is still a possibility of overwintering bacteria on the surface, but it’s not very likely.


Tomato Spotted Wilt Virus

Do you see the darkened borders on some of this foliage caused by small brown spots? That’s Tomato Spotted Wilt Virus. As with all virus-stricken plants, this tomato needs to be removed altogether and disposed of. (photo: Dr. Meg McGrath)


Knowing What You’re Dealing With

You may want to sit down for this: Identifying plant disease is extremely challenging. At times, even the experts struggle with picking the right pathogen out of a lineup. There are just so many of them out there, and often, they present the same symptoms.

Although you might not be certain which specific disease has hit your tomato, you can usually determine the type of pathogen – fungal, bacterial or viral. Each type has some common and subtly different markers.

Bacterial and fungal disease each tend to affect multiple plants simultaneously, while a virus usually manifests in a lone plant. Viral disease symptoms are more extreme, like distorted leaves or strange, mosaic coloration. Bacterial and fungal disease often manifest as yellowing or blackening leaves.


Gray mold plant disease

Yes, disease can be frustrating and destructive, like with gray mold’s effect on foliage as seen here, but it can also be pretty remarkable when you stop to appreciate the incredible diversity and power of nature. (photo: Dr. Meg McGrath)


Meg was extensively involved in development of an online resource designed to help home gardeners deal with plant diseases. It offers a wide range of valuable information, including plant clinics in every state. There is even an extensive library of photos and information on disease symptoms. Vegetable MD Online is another resource option, but that site is geared more toward commercial growers.

If you’re determined to know disease type, there are plant clinics available in every state (through your local County Extension office) which can test the diseased plant to identify the infecting pathogen.

I’ve got one raised bed that I suspect is infected with the soil-borne fungal disease Fusarium Wilt. If I can confirm the presence of a viral pathogen through testing, I’ll. know if I need to avoid growing Fusarium-susceptible plants in that bed in future seasons or if there’s another issue I have yet to identify.

Treating the Problem

The best treatment for disease is physical removal. Period. If you do opt to use a treatment product, know that even organic products carry risks – and sometimes those risks are serious.

Copper is an effective organic treatment for fungal and bacterial disease, however it can build up in soil over time and cause long term problems – including to the health of you and your family. It also presents some immediate and frightening health hazards. If you have copper on your hands after treatment and absentmindedly rub your eye, it can cause irreversible vision damage.

Copper is really the only effective treatment for bacterial disease. There are, however, a number of effective fungal treatments. Just be sure to read package instructions carefully and take precautions.

Meg doesn’t mess around when it comes to using treatments. Like me, she avoids using them in most instances, but when an extreme situation calls for any treatment product, she protects herself with gloves, boots, a respirator, and a Tyvek suit.


anthracnose on a tomato

Have you ever seen spots like these on your tomato fruit? These are the result of fungal anthracnose, which spreads easily and loves moist conditions. (photo: Dr. Meg McGrath)


It’s also important to know that not all products on the market work. Treatments available for sale in the U.S. have gone through an EPA approval process to evaluate them against certain safety thresholds, however the department does not test for efficacy or issue any efficacy standards.

That’s one of the reasons that Meg invests much of her professional time evaluating organic and synthetic treatment options. Many commercial growers rely on her reported results to determine what to incorporate in their treatment programs.

It can’t be stated often enough that treatment products do not cure disease – any disease. They only slow the spread. There are, however, some advancements in identifying treatments which can induce a plant’s own resistance to a particular disease.

Bacillus subtilis is one example. If applied before a disease has struck, it acts sort of like a vaccination. It tricks the plant into thinking it is being infected, which causes the plant to produce a defensive response. As a result, the plant is armed for when the disease actually does attack.

If your garden is hard hit by a fungal disease year after year, you may want to consider applying a fungicide early in the season. Proactive application can act as a protectant on foliage to prevent infection from taking place, but you will need to remain diligent with regular application.

There are no treatments or cures for viral diseases, so your only option is removal of the affected plant.


Late Blight disease

Seen here is an example of stem lesions from the very serious Late Blight disease. If you notice this on your tomatoes, don’t take chances – just pull the entire plant and dispose of it right away. (photo: Dr. Meg McGrath)


The Dangers of Late Blight

Here in the Atlanta area, I battle the fungal disease, Early Blight, regularly. Its spores travel on the wind, so it can be nearly impossible to keep out altogether. The fungal diseases you battle will depend on the typical conditions of the region in which you garden.

Late Blight, though, is a much more serious concern, and it can affect all of us. Don’t let the name fool you. Late Blight can come on at any time in the season. Meg has seen instances in her area as early as May. This is one disease you want to take very seriously. If you see any sign (like large leaf spots) or even just suspect its presence, destroy the plant.

2009 saw a serious outbreak of Late Blight all through the northeastern states of the U.S. Late Blight can pose a real danger to our food supply. It quickly wiped out the crops of farmers all through the region and had the agricultural industry sending out the alarm. The devastating effects continued throughout that season, and fortunately, there haven’t been wide-scale reports since.

If you grow potatoes, it’s important that you purchase certified seed potatoes only. Potatoes are carriers of Late Blight. In fact, this disease can’t overwinter or lie in dormancy on a piece of wood, it can only survive in a living plant. Infected seed potatoes have been known to trigger an outbreak in tomato plants. So although it’s tempting to start plants from potatoes you buy at the supermarket, they could be infected with Late Blight. Only by purchasing certified seed potatoes can you be confident that they are free of this devastating disease.


Late Blight disease

The appearance of Late Blight is relatively unique. Notice the damage spots on this tomato foliage? These show up quickly and will are larger in size than spots from most other diseases. (photo: Dr. Meg McGrath)


I hope this has been a good reminder that disease in your garden doesn’t signify failure. We can all take a cue from Meg and, instead, marvel at the wonders of nature that these tiny pathogens somehow find their way to their host plants in our garden. Meanwhile, we all do our best to keep them at bay with good proactive and management steps.

If you haven’t already listened to my conversation with Meg, you can click the Play icon in the green bar under the title at the top of this page. This is a topic that we all can benefit from hearing over and over again. Stay tuned for future plant disease podcast discussions with Meg.

Links & Resources

Episode 009: Organic Disease Control with Jeff Gillman

joegardener YouTube: How to Make the Ultimate Tomato Cage

joegardener Online Academy: Master Pests, Diseases and Weeds – my newest online course! Just $47 for lifetime access.

joegardener Newsletter

joegardener Facebook

joegardener Facebook Group

joegardener Instagram

joegardenerTV YouTube

joegardener Twitter


Vegetable Pathology – Long Island Horticultural Research & Extension Center, Cornell University College of Agricultural & Life Sciences

Photo Gallery, Tomato Diseases – Long Island Horticultural Research & Extension Center, Cornell University College of Agricultural & Life Sciences

Vegetable MD Online, Department of Plant Pathology, Cornell University

Soil Cubed – Our podcast episode sponsor and Brand Partner of

About Joe Lamp'l

Joe Lamp’l is the creator and “joe” behind joe gardener®. His lifetime passion and devotion to all things horticulture has led him to a long-time career as one of the country’s most recognized and trusted personalities in organic gardening and sustainability. That is most evident in his role as host and creator of Emmy Award-winning Growing a Greener World®, a national green-living lifestyle series on PBS currently broadcasting in its tenth season. When he’s not working in his large, raised bed vegetable garden, he’s likely planting or digging something up, or spending time with his family on their organic farm just north of Atlanta, GA.

0 Responses to “115-Understanding Tomato Diseases and How to Deal With Them”

  • Twitch132 says:

    Joe,First time gardener here up in Massachusetts. Have been utilizing all your articles and videos to try and figure this whole gardening thing out. Have had a pretty good season this far but a few weeks back I started seeing black spots on my tomatoes. I just listened to this podcast, checked Dr. McGrath’s website and think it is Bacterial Spect. My tomatoes are really starting to ripen now and I am just curious if they can still be eaten if they show any signs of Bacterial Spect. Any and all help is greatly appreciated.Respectfully,

  • Forrest Jones says:

    Hi Joe, I wasn’t sure if I should put this here or under 116. I purchased 4 varieties of tomatoes from my local garden store and grew 1 variety from seed. I did not ask yet but I suspect the store got all of their plants from the same grower. I planted some of each in landscape pots and grow bags filled with potting soil near the end of my driveway. I planted some of each in my garden beds a hundred feet away, which I made with native soil and the amendments of leaves and compost over the years. The variety called Carolina Sun Gold is not looking good at all in either location right beside the other varieties that are looking good in both locations. I don’t know if it is the same variety of sun gold that you grow.
    But what I am gleaming from this is that the problem has nothing to do with 2 completely different soils that never had contact at 2 somewhat widely spaced locations. All of the other plants are doing okay in both locations. I am leaning towards infected seed or some other problem not related to soil health at all. So I guess what I am trying to get at is that disease is not always a marker for soil health and we shouldn’t be quick to jump to that conclusion. So yes that is another one that I would like Dr. Ingham to speak about.Regards
    Forrest Jones
    Nanty Glo, Pennsylvania

  • Joe Lamp'l says:

    Such a great observation, Forrest and I agree with you. Your detective skills point to the seed. I will make a point of bring this up with Dr. Ingham. I think it is a fascinating question. Thank you.

  • Joe Lamp'l says:

    Hi Bobby. I hope by now you have been enjoying lots of tomatoes. You don’t need to worry about any risk of eating tomatoes infected with bacterial spot. You said the tomatoes are infected so did you mean the fruit or the leaves. It will affect both but still no reason to worry about health risk if you were to eat them. I know this is coming in late after you posted and I’m sorry I missed this right when it came in. Thanks for using my resources as guide. Just remember, every season is a growing experience. Learn from everything that happens. Good luck Bobby.

  • Sheila Schultz says:

    What should I do with the mulch that is under my tomato plants. If there is a fungus that caused blight, it would make sense to me to totally remove it from the garden and keep it out of the compost heap.

  • Joe Lamp'l says:

    I am a big believer in leaving the mulch in place and allowing it to breakdown to improve the soil with more organic matter. While it’s possible that the mulch could harbor fungus, there’s no way to know. And removing the mulch doesn’t preclude soil borne fungus from getting there other ways.Also there are many more good fungi than bad, and many are very effective at destroying bad fungi. So while you could take either route, I like the idea of assuming the chances are greater that my much is doing more to help, than the low risk that it is adding to the problem.Lastly, a fresh layer of mulch as you add new plants is always advisable anyway. Even if the old mulch contributed to an adverse fungal issue in some way, the new mulch is there in large part to cover the soil surface from whatever pathogens may be in the soil already.

  • Northwoods Dan says:

    I live in a rural area surrounded by potato farms that have struggled with late blight this season. Unfortunately, I couldn’t fight it off and my *container* tomatoes got late blight. I removed the plants and soil in trash bags and then bleached out the trash can after the garbage pick up came.I’m wondering what I have to do to clean my containers. Can they be cleaned? Can they be reused? I have cheaper “earthbox” style containers I grow my tomatoes in. I live in Wisconsin where winters are very cold. What should I do to ensure that my containers are clean and ready for tomatoes next season? Do I need to clean out flower pots near by that I grew everything from Johnny Jump-Ups to herbs and spices too? I grow blueberries in fabric containers. Do I need to replace those fabric containers too since they are with 5-10 feet?I can’t find reliable information on whether the containers can even be reused. Some say clean with bleach/water solution. Others say a cold winter will kill any spores.Any guidance? Obviously, I want to ensure this disease doesn’t come back next season. Of course, I’m all in on tomatoes, had a good season up until that point (got a big early harvest), and I’ll be back at it next year. I just want to be smart and thorough in preventing this from coming back next year.

  • Forrest Jones says:

    Joe, I have to walk it back. Over the last two weeks the rest of my beautiful tomato plants, 23 plants, with promising green tomatoes, were infected with late blight. I have no idea if it came form the Carolina Sun Golds that I removed a few weeks back. I think I am done with tomatoes. I suspect that the entire garden, grow bag and landscape pot soils are infected now. Far too much soil to replace with no guarantee that it wouldn’t happen again. I think I will just look for some interesting things to take the place of tomatoes. I did find Climbing Hydrangea but am still looking for Milorganite. Thanks for the update on season 10 of GGW.
    Nanty Glo, Pa

  • Joe Lamp'l says:

    Hi, Dan. So sorry to hear you got hit with late blight. That’s a nasty disease!
    If you submerge or soak your containers in a 10% or more bleach solution that will kill any disease pathogens. Between the bleach and the cold temps and empty, soil-free containers, you’ve done all you can. Those containers can be reused with proper sanitation. I’m emailing Dr. Meg McGrath to see if she has any other tips for you and others regarding your question. I’ll post her answer here in this tread whenever I hear from her. Thanks for your question Dan.

  • Joe Lamp'l says:

    OH NO! This is NOT good new, Forrest! I’m so sorry to hear this. Were you able to positively ID the problem as late blight? What a disappointment. Although I’ve yet to personally experience late blight on my plants, I dread the day. Sometimes I ask myself why do I even bother with tomatoes. They are by FAR the most labor intensive plants I grow! I think I’m a glutton for punishment I suppose. And lord knows I love a challenge. Please keep me posted. And If I grow tomatoes again next year (I’m sure I will), I’ll send you some of mine!

  • Forrest Jones says:

    I will send you a couple photos, I didn’t get around to removing them yet because there was nothing left to try to save. It looks like the blight in your photos.

  • Northwoods Dan says:

    Thank you for your response! Yeah, I’m not giving up. I don’t know that there was much else I could have done and it happens. I’ve been growing my own San Marzano tomatoes (and some other varieties) for years and this is the first season where I’ve had a problem. I’m going to dump all soil in all containers, bleach them all out, and leave them out for the winter.The most heartbreaking thing about late blight – speaking as a home gardener – is that you take care of the tomatoes all season, you get a bumper crop, and juuuusssttt before they go ripe this disease hits. Live and learn.I’m going to clean out all my containers, replace the soil next year, and give it another go next season. I’m curious if Dr. McGrath has any other advice. I’m in Central Wisconsin where late blight has been an issue for the past few years but this is the first time it has impacted my plants.I’ll take some pictures of the cleaning/sanitation process and keep you posted on how things go next season…Whether it works or doesn’t, I’d like for this to be helpful to others that may run into the same issue.LOVE the podcast and everything else went well this season including my container blueberries. Thanks for all the great advice and all the best to you and yours.

  • Joe Lamp'l says:

    You’re welcome, Dan. Knock on wood, I’ve never had late blight here but I’m sure it’s just a matter of time. As I read your part about the “worst part”, it made my heart sink. I know how you must have felt to lose those beauties on the one yard line, about to drive it in for a touchdown. So disappointing. I’m glad you’re not giving up! Keep me posted, please!

  • Vauna says:

    Thanks and This was very informative, My question is, would bleach kill the pathogens that can live from year to year on wooden stakes. I coordinate Fayette County, Georgia, MG Plant ARow for the Hungry and we use wooden stakes for support placing one stake between each plant and use the Florida Weave string method. We will transition to metal stakes in the future but cannot do it all this year! I really learned a lot from Dr Meg McGrath and all of your podcast! Thanks for any suggestions!

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