Common Tomato Plant Problems and How to Deal With Them

Common tomato plant problems and how to deal with them at a Southern California plant nursery.

Written by Susan B.

You don’t have to be an experienced vegetable gardener to try your hand at growing tomatoes. Nothing rivals the taste of a vine-ripened home-grown tomato. We talked about tomato terminology and varieties in a previous post. But we didn’t talk about diseases and other problems that affect tomatoes, or the solution to these problems. We will talk about some of the most severe diseases that gardeners face when growing tomatoes, what causes them, and what you can do to prevent them or address the issue before it ruins your entire harvest. 

Tomato Plant Diseases

Bacterial Canker

Clavibacter michiganensis is a naturally occurring bacteria that causes Bacterial Canker disease in tomatoes. The infection gets into the soil through infected plants. Garden tools that touch the infected plants can also contaminate the soil. The infection spreads when rain or overhead watering splashes the bacteria from the ground back up to plants. If insects damage plant stems, fruits, or leaves, the disease will spread through those open areas. Excessive pruning leaves bare spots on stems, and the bacteria can infect plants and spread from there. 

As tomatoes ripen and turn red, you may see yellow spots on the fruits. A black circle surrounds the yellow spots.

How to Prevent Bacterial Canker

Bacterial canker is a disease that contaminates the soil. Since many soil-borne diseases continue to thrive there, the best way to prevent future outbreaks is crop rotation. Remove diseased plants as soon as possible, and dispose of them in the trash, not your compost heap. Keep tomato plants away from the infected area for at least three years. 


The Colletotrichum phomoides fungus causes Anthracnose. It thrives in hot and humid conditions. The fungus spreads quickly through overhead watering and rain. When water hits the contaminated soil, it splashes the fungus back up to plants. The disease can also spread from plant to plant through the water.

How to Recognize Anthracnose

A dark circle that looks like a bull’s eye appears on the bottom or stem end of ripening fruits. The spot feels soft when you touch it. Upon cutting into the fruit, the mushy black area looks like rot. 

How to Prevent Anthracnose 

Keep an eye on your tomatoes to ensure that you pick them as soon as they are ripe. The disease is more likely to infect overripe fruits. More importantly, use a watering method that doesn’t allow water to splash upward. Soaker hoses or drip irrigation systems get the water to plant roots in a way that makes it impossible for the disease to spread from splashing water.

Early Blight

Alternaria solani is the fungus that causes Early Blight. The fungus contaminates the soil where it survives over the winter, If you have tomatoes that are infected with early Blight, it’s highly likely that your plants will continue to get infected with the disease if they’re planted in the same area. 

How to Identify Early Blight

The disease starts as brown spots develop on older plant leaves. Then a bull’s eye-like ring forms around the spot. The area around the brown spot turns yellow. Eventually, the entire leaves turn brown, and they fall off the plant. As the disease spreads, plants lose most, if not all, of their leaves. 

How to Prevent Early Blight

Treat infected plants with an organic fungicide as soon as possible. Early Blight can also infect eggplants and peppers, so avoid planting tomatoes, peppers, or eggplants in the same spot for several years. 

Septoria Leaf Spot

Septoria lycopersici is a fungal disease that spreads through tomato plant leaves. The infection only occurs after plants start producing fruits. In the early stages, the tomato plant’s lower leaves develop yellow spots with a dark gray dot in the center. A darker border surrounds the gray center portion of the spot. Eventually, black spots appear in the middle of the gray center of the original yellow spots. The leaves die and ultimately fall off the plant. 

How to Prevent

Avoid overhead watering because the spray from the sprinkler will spread the fungus from the leaves into the soil. Once the disease enters the soil, it continues to spread from there. Treat tomatoes with Double Nickel 55™ Fungicide and Bactericide. 

Fusarium and Verticillium Wilt

Fusarium and Verticillium Wilt are fungal diseases. The fungus is present in the soil where it infects young tomato plants through their roots. From there, the disease cuts off the flow of water and nutrients from the roots to the rest of the plant. The lack of water makes plants look like they are wilting during the day, although they look healthier at night. 

The wilting starts at the lower leaves, zapping their color before killing the foliage from the tips to the stems. After killing off the lowest leaves, the fungus moves upward, and ultimately it affects the whole plant. Both types of wilt attack heirloom tomato varieties that weren’t bred to resist the diseases. 

How to Deal With or Prevent the Problem

Don’t jump to conclusions when you see wilted tomato plants. If your plants have either disease, watering won’t help them. Check the soil for dryness before you water them. 

If you have diseased plants, remove them from the soil promptly. If you have an infected tomato plant in a container, remove the plant from the container and dispose of both the plant and the soil. Sterilize the pot before using it again. Don’t put diseased plants in your compost heap. 

Always look for plants that have labels that indicate they are resistant to wilt diseases. Plants labeled with a V are resistant to Verticillium, and plants labeled with F, FF, or FFF are resistant to Fusarium variations. 

More importantly, avoid planting eggplant, peppers, potatoes, or tomatoes in the location from which you removed diseased tomato plants for a minimum of four to six years. These fungal infections survive in the soil for many years – even when they don’t have a host plant to infect. 

We’ve highlighted some of the most severe diseases that affect tomato plants. Know that you can always come in or call us to talk to our garden experts if you suspect that your tomatoes are infected. Remember that many of these diseases survive for years in the soil. The key to preventing them from destroying your garden vegetables is keeping track of where you plant things from year to year. That will help you rotate planting spots ever year. 

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