A week ago, your tomato plants looked great, and you walked among them feeling a sense of satisfaction. Two days ago, there was something wrong. A few spots, maybe some yellowing leaves. Today it’s worse. And the creepy, suspenseful music starts playing in the background. The plot twist is coming for your home movie about tomato sauce, salsa, and tomato sandwiches. 

Nearly every gardener has at least one of the dreaded tomato disease issues, sometimes (like me) more than one. Learning how to recognize which it is can help you manage the disease and pick appropriate varieties to grow next year.

Septoria Leaf Spot

This fungal disease of tomatoes is common anywhere tomatoes are grown, and can eventually kill 100% of the crop. Unlike some other diseases, the fruit is not affected, which can be a significant differentiator when trying to diagnose tomato problems. Caused by the organism Septoria lycopersici, this disease affects tomatoes, as well as other plants such as eggplants and potatoes. 

The fungus is not soil-borne, but does overwinter in the decayed vegetation from the previous year’s crop lying on the ground. The disease starts to thrive in dense foliage, which causes lower airflow and higher humidity, resulting in leaves that stay wetter for longer periods. 

Identification of Septoria leaf spot

Typically, symptoms appear first on the older, lower leaves. Spots appear on the leaves, normally about ¼ inch in diameter, dark brown or black, and sometimes with a gray center. It’s that gray center spot that is key for identifying this disease. Eventually, the spots merge together, the leaf turns yellow and wilts, and drops off. 

Fortunately, the fruit is not affected, and normal-looking fruit on a sickly-looking tomato whose foliage is covered in spots is a good start in identifying this disease. Yields will be reduced, but you may still get a partial crop.

What to do about Septoria leaf spot

Your best bet is to be vigilant about garden sanitation in the fall, move your tomatoes to a new patch of garden if you’ve had a problem in the previous year, and maintain vigorously growing plants.

• Increase the spacing between plants to allow for adequate airflow. Pruning tomatoes can also help prevent excessively dense foliage.

• Remove infected foliage as soon as you see it and burn or dispose of it. Don’t compost it or leave it lying in the garden.

• Water at the base of the plants, or if you water overhead, only water in the morning to allow the leaves to dry before nightfall.

• Fungicides labeled for vegetables are not very effective at control once symptoms have been noticed, but are somewhat effective at prevention.  

Early blight 

Early blight is another fungal disease affecting tomatoes and plants in the tomato family, such as peppers, potatoes, and eggplants, and is caused by fungi in the Alternaria genus. It can resemble Septoria leaf spot, several tomato wilting diseases, and bacterial problems. 

This fungus is soil-borne, overwintering in old infected plant debris and in the soil. Plants become infected when their leaves come into contact with the soil (a good reason to prune tomatoes) or when soil splashes up from the surface onto leaves through rain or irrigation. 

Rainy or humid weather, wet leaves from heavy dew, and warm summer temperatures are the perfect conditions for this disease to spread. 

Identification of Early Blight

You’ll see early blight start at the bottom of the plant, with the lowest leaves, and work up from there. Small dark spots form on the lower leaves, but unlike Septoria, these can grow to be half an inch in diameter. If you look closely at the spot, you may see concentric rings like a bullseye. Leaves eventually turn yellow, then brown, and wilt. They may or may not fall off the plant. 

A key identifying feature of early blight is that the fruit is also frequently infected, and it will have dark brown, leathery spots near the stem end, which may cause it to drop from the plant. 

What to do about Early Blight

Fortunately, many tomato varieties are now resistant to early blight, and that’s your first and best defense. A resistant variety can still get early blight, but the disease will spread more slowly, and the plant can often grow faster than the disease can kill it, allowing you to still get a harvest.

• Mulch under tomatoes to prevent soil from splashing up onto the leaves. 

• Irrigate from below the leaves at the base of the plant with a drip line if possible.

• Prune off lower branches with leaves that touch the ground.

• Stake plants and space them adequately to increase airflow.

• Remove infected foliage and burn or dispose of it. Don’t compost it.

Bacterial Speck and Bacterial Spot

Bacterial speck and bacterial spot are common diseases of tomatoes in all areas where gardeners grow tomatoes. Although caused by two completely different bacteria, the symptoms and end results are very similar. 

Both diseases flourish in warm, wet weather and affect all above-ground parts of the plant, including the fruit. Both diseases can overwinter in crop residue left in the garden if they were present the year before. 

While fungal diseases can spread on the wind, bacterial speck and bacterial spot are most commonly introduced to your garden from contaminated seed or via transplants purchased at the garden center, which haven’t yet begun to show symptoms. 

Identification of Bacterial Speck and Bacterial Spot

These two diseases are easily confused with each other, but for gardeners, it isn’t really necessary to differentiate between them. The effects on our tomatoes are the same, and so is the management.

Look for small, dark brown or black spots, about 1/8 inch in diameter, sometimes surrounded by yellow rings. Spots, also called lesions, can occur on the leaves and stem first, and eventually on the fruit. Fruit infected will display small brown or black spots, which may have a darker green ring around them on unripe fruit. Eventually, leaves may wilt and fall off. 

While bacterial speck and spot can look remarkably similar to Septoria leaf spot, remember that Septoria doesn’t infect the fruit, and often has light gray dots at the center of the brown leaf spots. These bacterial diseases will infect the fruit like early blight, but with tiny black spots, not large leathery lesions.

What to do about bacterial speck and bacterial spot

Unfortunately, a tomato plant infected with bacterial speck or spot cannot be cured. Varieties resistant to bacterial speck are uncommon, and currently, no commercially available cultivars are resistant to bacterial spot. That means your best defense is a good offense by limiting opportunities for spreading.

• Avoid overhead irrigation if possible. Splashing bacteria from leaf to leaf can spread the disease to uninfected plants.

• Don’t handle plants when they’re wet, for example early in the morning when they are still wet with dew.

• Sanitize your tools between tomato plants (always a good idea!) with 70% isopropyl alcohol or a 10% bleach solution.

• Remove infected plants and burn or dispose of them. Don’t compost them, and don’t leave them lying around in the garden. 

• Don’t eat the infected fruit.

• Do a diligent job of removing all tomato debris at the end of the garden season. These bacteria can overwinter on plant residue, but don’t survive on soil without tomato detritus.