Tomato Black Spot ID: What’s That Spot From?

What exactly causes tomato black spot and how do you fix it? We discuss a host of spotting-related issues that could be the culprit.

Tomato black spot on leaves caused by anthracnose


If you’ve grown tomatoes, you know about the dreaded tomato black spot. But did you know that tomato black spot isn’t relegated to one particular cause? Sometimes it’s a disease, and sometimes it’s not a disease. Sometimes the cause of infected fruit is from infected plant debris, other times it’s pests or weather conditions. 

It can be disheartening to see black spots on your tomato plants and tomato fruit. But it’s not the end of the world. Because tomato fruit can be very prolific you probably have enough time to remedy the issue.  

Whether it comes down to a pest, disease, or nutrient issue, most black spot problems can be dealt with. So let’s discuss the causes of black spot and how you can provide countermeasures to combat the issue. That way you can prevent the spread of disease to other plants, and have delicious fruit all year round. 

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So, You Have Black Spots. Now What?

Tomato black spot on leaves caused by anthracnose
Anthracnose can be one cause of tomato black spot on leaves and fruit. Source: cristina.sanvito

The vast majority of black spots on a tomato plant can be dealt with and treated. So if you see tomato plants in your garden that have spots on the leaves or affected fruits, do not fret. Identify the cause of the problem, and act accordingly. Developing fruit will most likely be safe from future black spots. There are only a few conditions in this piece that require drastic measures. Most of them can be prevented by spreading a thick layer of mulch at the base of the plants. 

When the tomato growing season starts and your tomato plant is transplanted and becomes established, add some shredded leaves, straw, or bark mulch to help retain soil moisture and prevent the conditions that cause black spots. Consider growing Mountain Delight, a highly disease-resistant plant that produces plentiful amounts of fruit in a season. Growing more fruit means a better harvest, even in the face of pestilence and unfavorable conditions. 

Diseases that Cause Black Spot

Here are the most common diseases that cause black spots on tomatoes. This section discusses how tomato gardeners can identify the disease type, and how they can mitigate the effects of the disease in question. 

Fungal Diseases

Anthracnose is commonly known as early blight. It causes spots on the leaves of tomato plants. It originates from a collection of fungal pathogens that attack several plants. Because these pathogens spread via spore, a healthy plant can obtain an infection by simply being downwind from affected plants. The fungi that cause the disease are most active in temperate spring and summer. Once things heat up, the conditions in which anthracnose fungi thrive lessen. Later stages of the disease cause sunken patches on the tomato fruits. 

Sometimes the fruit lesions are discolored and sometimes they aren’t. The spots can spread to tomato plant stems and spore masses can develop on the entire plant. Meanwhile, new growth is distorted. One of the best treatments for this disease is neem oil because it kills the fungal growth before it can progress. Sprays with Bacillus subtilis are effective as well. The bacterium outcompetes other soil microbes, eliminating any of the anthracnose spores that may have nestled into the soil line. Copper fungicide and sulfur dust fungicide are also highly effective against anthracnose. But aim for prevention. Remove diseased leaves and fruit and destroy them. Ensure your tomatoes are properly staked and use a drip line to prevent movement through water by the spores. Mulch and rotate crops to prevent overwintering of the disease. 

Anthracnose fruit rot
Colletotrichum coccodes causes anthracnose leaf spot and fruit rot in tomatoes. Source: Clemson University

Septoria causes black spots on tomatoes, especially on the lower branches of the plant. It’s caused by the fungal pathogen, Septoria lycopersici, which spreads via infected plant material that is buried under the soil. Nearby weeds can spread the septoria leaf spot as well.

While the tomato leaves take on brown spots at first, as the spores develop, the center of each septoria leaf spot blackens. Later stages of septoria leaf spot in tomatoes can cause dark patches on plant stems. Fruit is rarely affected. 

As with many diseases, remove infected plant material from the garden as soon as possible. Use copper and biological fungicides to prevent the spread of septoria leaf spot to other parts of the plant. If these aren’t effective, there are chemical fungicides on the market that can eliminate the problem. Prevention of septoria leaf spots involves mulching, using drip irrigation, and rotating crops. Because some pests spread septoria leaf spot, keep them at bay. Overall, septoria leaf spot is not difficult to treat or prevent. 

Fusarium wilt or Verticillium wilt might look a lot like early blight, but they’re feeding on the roots of the plant first, rather than the leaves. The fungal disease Fusarium oxysporium sp. Lycopersici causes fusarium wilt on tomatoes, while Verticillium dahliae causes verticillium wilt. Both create spots on the leaf tips of growing tomatoes after they begin feeding on the tomato plant root system. Remove any plant debris that takes residence in the soil around the base of your plants. Also, remove affected leaves and branches, and practice crop rotation. Keep the soil evenly moist and not waterlogged to prevent optimal conditions for wilt. There are tons of wilt-resistant varieties of tomatoes you can plant as well. Certain mycorrhizal material can keep the fungi that cause wilt at bay too. 

Alternaria leaf spot and Alternaria canker are caused by Alternaria genus fungi. The symptoms of the latter disease include stem lesions with pronounced concentric rings. Other symptoms in the later stages of Alternaria infection include girdled plants that are caused by collar rot. Overhead irrigation, rainy weather, and the overwintering of spores on infected leaves and volunteer plants are the main culprits for this disease. While there are many chemicals and copper fungicides available that can treat and prevent black spots of this kind, it’s easiest to control the concentric rings of Alternaria canker through prevention. Irrigate at the base of your tomato plants, rather than overhead. Plant disease-free seed and resistant varieties. 

Bacterial Diseases

Bacterial speck causes raised, tiny black spots on green tomatoes. This springtime disease is caused by the bacterium, Pseudomonas syringae pv. tomato. It moves through water splashes, or via infected gardening tools. Two of the best ways to prevent bacterial speck are to sanitize your tools between uses and employ drip irrigating systems. Bacterial spot is caused by 4 different species of Xanthomonas bacteria. It causes black spots that are larger and more raised than that of bacterial speck. 

Both cause blotchy leaves on infected plants and stem spotting in late infection stages. Defoliation in both cases makes tomatoes more susceptible to sunscald. Damage to fruit can allow the entry of secondary organisms into the wounds, worsening the problem. Neither of these bacteria can be combatted, which is why prevention is key. One of the best forms of prevention is to water tomato plants with drip irrigation. Try copper-based sprays to prevent the development of these diseases. Always sterilize your tools. And remove infected plants and destroy them. 

Oomycete Diseases

Phytophthora on tomato stem
Phytophthora (late blight) on tomato stem. Source: photofarmer

Phytophthora is a water mold disease that is commonly referred to as late blight. It spreads rapidly through the soil in damp and humid conditions. It causes blotchy, curling leaves, and large spots on tomato fruits. The zoospores of this pathogen move between water pores below the soil line and feed on the roots of tomato plants. Improve soil drainage, and control moisture fluctuation to prevent the rotting of tomato roots. Grow a late blight-resistant tomato variety and rotate your crops. Some fungicides can be used preventatively before signs of the disease show. 

Viral Diseases

Tomato spotted wilt virus, like Alternaria canker, causes concentric rings, but not on leaves. Instead, the rings develop on tomato fruits. They are light yellow at first but then develop into a necrotic brownish-black spot that renders the fruit inedible. The easiest way to control the viral spread is to control thrips – common tomato pests that feed on all parts of the plant, especially the first bloom of the season. Use insecticidal soap if you notice thrip damage on your plants. Plant resistant varieties. Because there is no treatment for the virus itself, the entire plant must be removed and destroyed when it is detected. 

Pests That Cause Black Spot

Aside from thrips, other pests can cause black spots. Tomato hornworm damage may not cause black spots on tomatoes right away, but eventually, the wounded ripe tomatoes will blacken. This has to do with the susceptibility of tomato fruits that can become infected by fungi and bacteria that make their way to the wound. So controlling tomato hornworms on your plants can assist you in preventing black spots on tomato fruit. 

Usually, these caterpillars are easy to see. They can be picked off the plants by hand, and given to chickens or turkeys. They’re nightshade lovers and can be relocated if you’d like to encourage pollination by the adult version of the tomato hornworm: the five-spotted hawkmoth. If you want to remove them completely, Bacillus thuringiensis (Bt) sprays kill them. 

Conditions That Cause Black Spot

Blossom end rot
Blossom end rot is a failure of the plant to absorb calcium. Source: eggrole

The most common and notable of all black spot conditions is tomato blossom end rot.  While the condition may look very severe, it’s something that can be easily remedied. The primary cause of tomato blossom end rot is a calcium deficiency, but there are a set of physiological conditions that occur before difficulties in calcium uptake occur. Moisture fluctuations, imbalances in the soil pH level, too much fertilizer, improper additives (such as Epsom salt, which contains no calcium at all), and high salinity soil conditions all lead to difficulties with calcium absorption. That lack of calcium absorption causes blossom end rot. While applying more calcium might seem like the right move, you really need a remedy that’s holistic and considers all parts of your tomato plants and fruit; if it doesn’t repair the actual issues (which are often feast-or-famine watering conditions or the application of excess fertilizers), the blossom end rot will just continue no matter how much calcium you pump into the soil.

As long as you catch this condition on your tomatoes early by monitoring each blossom end, there should be no problem at all. Keep the soil consistently moist at all times, and avoid letting it completely dry out between waterings or going overboard with pooling moisture. If you have difficulties with low pH soil, perform a soil test to determine where any imbalances are and to determine how to amend it to support the blossom end of tomato plants. Most of the time a good dressing of compost each growing season is adequate, and you won’t have to add calcium products like calcium nitrate or calcium chloride. An excess of nitrogen based fertilizers or overapplication of other fertilizers can cause issues with the condition as well. But it’s not just too much nitrogen that’s the issue; too much calcium can prevent its uptake, too! Instead of reaching for a calcium spray to prevent blossom end rot, determine what the actual cause of the blossom end rot is. Calcium sprays or crushed eggshells provide little to no benefit in resolving the actual problem.

You may have also heard about mixing water and Epsom salt in a spray bottle to combat blossom end rot in most soils. The truth is that magnesium sulfate sprays don’t prevent blossom end rot, and can make the problem worse by glutting the soil with magnesium. Ensure the conditions in which you planted the tomatoes provide enough support to help them absorb calcium from the get-go. Healthy roots and undamaged root systems also keep blossom end rot at bay. Prevent pests and diseases that feed on tomato plant roots, make sure you don’t have a soil condition that is wreaking havoc, and ensure you keep things damp during dry weather, and you’ll have a healthy blossom end that provides lovely tomato fruit. 

Another condition that causes black spots on a tomato plant is frost damage. If you have your tomato plants out in the garden at the end of the growing season in fall, a snap freeze can produce blotchy, dark green patches of frost damage. The dark green damage turns to brown spots, and finally, dark black frost damage sets in. It can spread, too. Remove the parts that take on damage as soon as possible. While it’s possible to provide a physical barrier to protect plants in light freezes when cold weather sets in, you should remove your tomato plants from the outdoors. You can overwinter them indoors or in a greenhouse. You can also cut the plant down a few inches above the ground, and spread a thick layer of mulch to protect them in cold. 

Frequently Asked Questions

Early septoria leaf spot on tomato
Early stages of septoria leaf spot in tomato. Source: cristina.sanvito

Q: How do you treat black spots on tomatoes?

A: It depends! You’ll have to identify what the black spots are on your tomatoes first. 

Q: Are tomatoes with black spots safe to eat?

A: One rule of thumb is to avoid long-term storage of tomatoes that are spotted. If you would like to see if the fruit can be used fresh, cut it open to see if damage has spread to other tissue. Brown spots from mold in fruit are an indication it’s not edible. So is fruit that is dry and fibrous within.