Tomato Plant Turning Black: Fruit, Leaves, Stems? (6 Tips)

If you see black spots on your tomato plants, you are not alone. You may find the fruit, leaves, or stems of tomato plants turn black during a growing season – luckily, the location of the black spots can help you to find the source of the problem.

So, why is your tomato plant turning black? Black spots on tomato fruit are caused by blossom end rot, buckeye rot, anthracnose, bacterial spot, & sunscald. Black spots on tomato leaves are caused by early blight, late blight, bacterial speck, & sooty mold. Black spots on tomato stems are caused by bacterial wilt, alternaria stem canker, & tomato pith necrosis.

Sometimes, these problems look the same, so it might take a little work to find the exact cause of black spots on your tomatoes.

In this article, we’ll examine the many causes of black spots on tomato plants. We’ll also give you some ideas about how to prevent this from happening in your garden.

Let’s get started.

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Why Is My Tomato Plant Turning Black On The Fruit?

There are many different causes of black spots on tomato fruit, including:

  • nutrient deficiencies
  • bacteria
  • viruses
  • mold
blossom end rot on tomato plant
There are lots of different reasons that tomato plants turn black. The fruit, leaves, or stems may be affected.

Let’s start by taking a closer look at a common tomato problem that results in a nutrient deficiency from uneven watering: blossom end rot.

Tomato Blossom End Rot

Blossom end rot affects tomatoes, but it also affects peppers and eggplants (all of these plants are in the nightshade family, Solanaceae).

Blossom end rot first manifests as sunken, decaying areas on the bottom of a tomato fruit. These sunken areas on the fruit eventually turn dark brown and then black.

A brown and black spot appears at the bottom of tomatoes on plants suffering from blossom end rot.

For more information, check out this article from Wikipedia on calcium deficiency and blossom end rot.

According to the University of Wisconsin Extension, blossom end rot is caused by a calcium deficiency in the plant. This can occur for several reasons:

  • Insufficient calcium in the soil. You can treat this problem with lime (calcium carbonate) or other calcium supplements (such as dolomite lime, which also provides magnesium).
  • Too much nitrogen in the soil. This could be caused by excessive use of manure or other nitrogen-rich fertilizers. You can prevent this problem by using low-nitrogen fertilizers. On a fertilizer package, N-P-K is clearly stated (for example, 10-10-10). The first number is the percent by weight of nitrogen – look for a lower number to get less nitrogen. For more information, check out my article on over fertilizing plants and my article on low-nitrogen fertilizers.
  • A pH imbalance in the soil.  If soil pH is too low or too high, a tomato plant will have trouble absorbing calcium through its roots, even if there is plenty of calcium in the soil. You can treat this problem by correcting pH with either lime (to raise pH) or sulfur (to lower pH).
  • Inconsistent watering (too little followed by too much). Check the weather forecast to avoid watering before rainstorms. Also, check the soil with your fingers for dryness before watering.

Before adding any amendments to your garden, you should do a soil test to determine if your soil has nutrient or pH imbalances. For more information, check out my article on how to do a soil test.

Buckeye Rot

Buckeye rot is a fungal disease that affects tomato fruit. It is caused by the fungi Phytophthora parasitica, Phytophthora capsici, and Phytophthora drechsleri (Buckeye rot also affects pepper plants).

Buckeye rot starts out as brown spots (lesions) on the tomato. This is more common if the fruit was touching the soil.

The brown spots on the fruit get larger over time. Eventually, darker brown or black rings appear.

The lesions caused by buckeye rot tend to stay smooth and firm as the disease progresses. With time, the entire fruit will rot.

If weather conditions are moist (from rain or high humidity), a white fungus that looks like cotton may grow on top of the lesions.

Buckeye rot is spread by rain and by water on the surface of the soil.

For more information, check out this article from Clemson University on Buckeye Rot and other tomato disorders.


Anthracnose is a fungal disease that damages tomato fruit, but not leaves. It is caused by the fungus Colletotrichum coccoides (Anthracnose can also affect peppers and eggplants).

When infected tomatoes ripen, you will first see small circular dents on the fruit. Later, the center of these circular dents will get darker and larger.

antrhacnose on tomato fruit
Anthracnose is caused by a fungus that affects tomato fruit (but not leaves) by causing round dents that get darker and larger.
Image Courtesy of:
Clemson University via:
Wikimedia Commons: https://commons.

In humid weather, you may see pink spores on top of the dents. According to Clemson University, these spores spread to other plants by splashing water from rain or irrigation.

For more information, you can check out this article from Michigan State University on Anthracnose (and other tomato disorders).

Bacterial Spot

According to Clemson Univeristy, Bacterial spot on tomato fruit is caused by the bacteria Xanthomonas perforans. Interestingly, this disease attacks green tomatoes, but not red ones (it can also affect pepper plants).

Affected plants will display raised spots (scabs) on the fruit. You may also see small spots with irregular shapes on the leaves.

This disease thrives in wet weather, and it often spreads after a rainstorm. Fruit is infected when insects or animals puncture the skin of the fruit.

Bacterial spot can infect a tomato plant’s leaves without such damage occurring.

For more information, check out this article from Clemson University on Bacterial spot and other tomato disorders.


Sunscald occurs when tomato fruits are exposed to excessive amounts of direct sunlight. According to the Michigan State University Extension, both green and ripe fruit can develop sunscald spots.

Normally, the leaves of a tomato plant will block or absorb the light from the sun. This prevents the brunt of the sun’s intense rays from getting to the fruit.

However, if a tomato plant has suffered from poor nutrition or defoliation (due to pests or over pruning), there may not be enough leaves to protect the fruit from the sun.

Sunscald first appears as white, tan, or gray blisters on the tomato fruit. Normally, sunscald occurs on the sides of the fruit.

sunscald on tomato
Sunscald appears as a white, tan, or gray blister on the skin of a tomato fruit. Black mold may later grow on the spot.

Typically, sunscald happens to fruit on the side of the plant that gets the most sun (or has the fewest leaves).

Eventually, black mold will grow in sunscald patches on tomatoes, which explains the black spots you later see on the fruit.

For more information, check out this article from Wikipedia on sunscald.

Why Are My Tomato Plant Leaves Turning Black?

The fruit isn’t the only part of a tomato plant that can turn black due to disease. The leaves can also turn black for various reasons.

The problems that can cause black spots on tomato leaves are numerous. Let’s look at some of the common ones you might see – starting with early blight.

Early Blight

Early blight can be caused by two types of fungi: Alternaria tomatophila and Alternaria solani (it can also affect potatoes). You will first see small brown spots, usually on older tomato leaves (lower on the plant).

early blight on tomato leaf
Here, we can see some dark spots of early blight on tomato leaves. Image from:

Eventually, the spots will get larger and you will see concentric circles forming, almost like a bullseye pattern. You may also see black, leathery spots on the tomato fruit.

Generally, early blight develops in warm temperatures, from 59 to 80 degrees Fahrenheit (15 to 27 Celsius). Early blight is a fungus, so high humidity levels (90% or greater) also encourage its growth and spread.

According to the Michigan State University Extension, early blight can survive over the winter in plant debris and seeds. So, volunteer tomato plants may not be something you want if early blight is a problem in your garden!

For more information, check out this article from Clemson University on Early Blight and other tomato disorders.

Late Blight

Late blight can infect both tomatoes and potatoes. In fact, it was responsible for the Irish potato famine of 1840.  It is caused by the fungus Phytophthora infestans.

late blight on tomato stem
Here we can see spots of late blight on a tomato stem. Image from:

Late blight can affect all parts of the tomato plant.  On the leaves, the disease first appears as small, dark spots.

Eventually, these spots get larger, and white mold will grow on the edges of the spots. You may also see dark, shiny, firm lesions on the tomato fruit.

Lesions can also grow on tomato stems and quickly kill them. Of the two types of blight, late blight is more deadly to tomato plants.

According to the Michigan State University Extension, late blight thrives in cool, moist weather.

For more information, check out this article from Clemson University on Late Blight and other tomato disorders.

Sooty Mold

Black sooty mold is a dark mold that looks like soot (from a chimney) that covers leaves (and sometimes, the stems) of tomato plants. You can tell your plant has black sooty mold if you can scrape away the mold or wash it away with water.

sooty mold
Here we can see sooty mold – it is not a tomato plant, but the appearance of the black mold would be the same on tomato leaves.

For more information, check out this article from Mississippi State University on black sooty mold.

Black sooty mold is caused indirectly by tiny insects called aphids.

First, the aphids feed on tomatoes (or other plants). As they do so, they suck the juices out of the leaves and stems.

Aphids suck the juice out of plant leaves and stems, leave behind honeydew, and sooty mold grows on the honeydew.

Next, the aphids digest the plant juices, leaving behind honeydew. This sticky, sweet waste product provides the perfect energy for sooty mold.

Then, as sooty mold grows on the honeydew, it spreads to cover the leaves and stems of the tomato plant (anywhere the aphids have left their waste).

To prevent sooty mold from affecting your tomato plants, take steps to get rid of aphids in your garden. One way is to spray them with a combination of water, dish soap, and alcohol.

For more information, check out my article on how to get rid of aphids.

Septoria Leaf Spot

According to the Michigan State University Extension, Septoria Leaf Spot is caused by the fungus Septoria lycopersici. It usually affects older leaves on the tomato plant (the ones closer to the ground).

In some cases, Septoria leaf spot can also affect the stems of tomato plants.

The first sign of Septoria leaf spot is the appearance of many small, circular spots with dark edges on leaves. You will also see smaller black areas in the center of the circular spots.

septoria leaf spot on tomato leaves
Septoria leaf spot causes small black areas (that hold spores) in the center of circular spots on tomato leaves.
Image Courtesy of:
Dr Parthasarathy Seethapathy,
Tamil Nadu Agricultural University, via:
Wikimedia Commons:

These black areas produce spores to spread the fungus to other nearby plants. Rain or overhead watering that wets the leaves will help Septoria leaf spot to spread.

Leaves that are severely affected may turn yellow and fall off the plant. In extreme cases, a lack of leaves due to Septoria leaf spot will lead to sun scald (see the description earlier in this article).

In this way, Septoria leaf spot will indirectly affect tomato fruit.

For more information, check out this article from Clemson University on Septoria Leaf Spot and other tomato disorders.

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Fusarium Wilt

Fusarium wilt is caused by the fungus Fusarium oxysporum. The first sign of this disease that you will see is wilted “lazy” leaves on the lower part of the tomato plant.

The leaves may eventually turn yellow, brown, and black as necrosis (tissue death) sets in. The stems will also show browning if they are cut lengthwise.

fusarium wilt on tomato plant
Fusarium wilt causes yellow, brown, and black wilted leaves on tomato plants.
Image Courtesy of:
Victor M. Vicente Selvas
via: Wikimedia Commons: https://commons.

For more information, check out this article from Clemson University on Fusarium Wilt and other tomato disorders.

Verticillium Wilt

Verticillium wilt can be caused by 6 different species of Verticillium fungi.  s with fusarium wilt, the first sign is wilted leaves, and possibly wilted stems.

This wilting is caused by the disease affecting vascular tissue in the plant. According to the North Carolina State University Extension, this vascular tissue helps the plant to move water and nutrients.

Often, the disease will affect only one side of a plant, moving up through the stems instead of around the stem.  Eventually, you will see yellowing leaves (chlorosis) followed by browning or blackening and death of plant tissue (necrosis).

Tomato Spotted Wilt Virus

Tomato Spotted Wilt Virus is spread to tomato plants when the thrip (a tiny insect) feeds on plants already infected with the virus.  Some of the first signs of Tomato spotted wilt virus are stunted growth, dark spots on leaves, and purple veins.

thrips tomatoes
Thrips are tiny insects that spread Tomato spotted wilt virus when they move between plants to feed.

The younger leaves (higher up on the plant) may twist and curl as the dark spots on the leaves grow larger.  A plant that survives may go on to bear fruit with dark, black spots all over it.

For more information, check out this article from Clemson University on Tomato Spotted Wilt Virus and other tomato disorders.

Tobacco Mosaic Virus

Tobacco mosaic virus causes mottling and black areas on the leaves of tomato plants.  The virus is spread by plant sap, and there is no known cure.

It can affect nightshade plants including tomatoes, peppers, eggplants, and potatoes.

Infected plants should be removed and destroyed.  Also, be sure to avoid working with your plants after touching or using tobacco products (such as chewing tobacco, cigars, cigarettes, etc.)

For more information, check out this article from the University of Massachusetts on tobacco mosaic virus.

Herbicide Damage

Herbicides can also damage tomato plants and cause damage or death of leaves.  If you live near a commercial farm, this is more likely (the wind can carry these herbicides some distance to your yard).

Leaf Mold

Leaf mold is caused by the fungus Passalora fulva.  The mold first appears on older leaves, lower on the plant and close to the soil.

leaf mold on tomato
Leaf mold is caused by a fungus that appears on the older (lower) leaves on a tomato plant.
Image Courtesy of:
Elizabeth Bush, Virginia Polytechnic Institute and State University via:
Wikimedia Commons: https://commons.

These lower leaves are more likely to get wet from overhead watering or splashing rain.  They are also more likely to stay wet, since higher leaves on the plant prevent sunlight from drying out the lower leaves.

Leaf mold starts out as pale green or yellow spots on the top of the leaf.  These spots get larger and turn darker, eventually becoming brown or black.

The spores of leaf mold can be spread by rain, wind, or tools, so be sure to wash and sterilize your equipment between plants.

For more information, check out this article from Clemson University on Leaf Mold and other tomato disorders.

Why Are My Tomato Plant Stems Turning Black?

There are a few tomato problems that can cause black spots on the stems.  Let’s take a closer look at those now, starting with Bacterial wilt.

Bacterial Wilt

Bacterial Wilt is caused by the bacteria Ralstonia solanacearum.  This bacteria gets into tomato plants through injury sites in the roots.

tomato bacterial wilt
Tomato bacterial wilt gets into tomato plants through injury sites in the roots.

These injury sites are made by insects or by gardeners when transplanting seedlings.

Warm and moist climates will promote the growth of bacterial wilt. So, it is more likely to grow on tomato plants raised in a greenhouse with high humidity and frequent watering.

For more information, check out this article from Clemson University on Bacterial Wilt and other tomato disorders.

Alternaria Stem Canker

Alternaria Stem Canker is caused by the fungus Alternaria alternata.  It lives in tomato seeds and seedlings, and it is spread by airborne spores (the more wind, the more likely it is to spread).

Alternaria Stem Canker causes brown or black spots on the stems of infected tomato plants.  The leaves of an infected plant may also turn yellow or brown, with older (lower) leaves affected first.

Alternaria spores can even cause respiratory infections and asthma in humans, so be careful if you find it in your garden.

For more information, check out this article on Alternaria Stem Canker from Wikipedia.

Tomato Pith Necrosis

Tomato Pith Necrosis is caused by many species of the Pseudomonas bacteria.  These soil-borne bacteria infect tomato plants on cloudy, cool, moist days.

The early signs of Tomato Pith Necrosis are black, necrotic spots on the stems.  Eventually, these spots become larger and grow along the stem.

In time, the stems will become hollow.  Parts of some tomato leaves may also turn black as a result of Tomato Pith Necrosis.

For more information, check out this article from Clemson University on Tomato Pith Necrosis and other tomato disorders.

How To Prevent Tomatoes From Getting Diseases

There are many diseases that could cause your tomato plants to turn black.  Luckily, there are also some steps you can take to prevent these problems.

Choose Disease Resistant Tomato Varieties

One of the best ways to avoid disease in the first place is to choose disease resistant tomato varieties. The seed catalog description of a tomato variety will often indicate resistance to common diseases, such as:

  • Fusarium Wilt (F)
  • Verticillium Wilt (V)
  • Early Blight (E or EB)
  • Late Blight (L or LB)
  • Tomato Spotted Wilt Virus (TSWV)

If you find that you have difficulty with a specific tomato disease in your garden, look for varieties that have resistance to that disease.

Use Crop Rotation

Crop rotation means that you do not plant the same crop in the same part of your garden for two years in a row.  Preferably, you rotate the crops on a 3 or 4 year cycle.

This helps to prevent diseases from establishing a foothold in your garden.

tomatoes and potatoes
Don’t plant tomatoes and potatoes in the same place in alternating years, since they share many of the same diseases, including early blight and late blight.

Tomato plants become infected with many of the same diseases as peppers, eggplants, and potatoes (all are in the nightshade family).

Thus, you should avoid planting any of these crops in the same area two years in a row (that is, don’t plant potatoes right after tomatoes in the same spot in your garden the next year).

You can learn more about good crops to rotate with tomatoes in my article here.

Do Not Wet The Leaves On Your Tomato Plants

Water your tomato plants close to the soil, not from above.  This prevents water from splashing soil up onto the lower leaves, which is where many diseases start.

tomato plants with twine rope stake
Avoid wetting the leaves of your tomato plants to prevent fungus from growing and spreading.

It also prevents the leaves from getting wet, which helps to discourage the growth and spread of mold and fungus.

Leave Enough Space Between Tomato Plants

If tomato plants do become infected, it is easier to prevent the spread of disease if your tomato plants have adequate spacing.

Plant tomatoes at least 18 to 24 inches apart. Try to prune wandering branches so that the leaves or branches from neighboring plants do not touch each other.

tomato stakes
Leave enough space between tomato plants to prevent the spread of disease if one plant does get infected.

Leaving enough space between plants also means that splashing water from rain is more likely to infect only one plant, rather than multiple plants at once.

Remove The Lower Leaves Of Your Tomato Plants

Many diseases start in the soil and make their way onto tomato plants when water splashes soil onto the lower leaves.

pruning shears
Prune the lower leaves from tomato plants (after they are established) to prevent soil diseases from splashing up during rain or watering.

In light of this fact, it is a good idea to prune off the lower leaves once your tomato plants are established.

Remove & Destroy Infected Plants

Once a plant becomes infected, there is likely no cure. In most cases, the safest course of action is to pull up the plant and destroy it by burning.

This might seem like a waste, but composting the plant presents the danger that a disease will survive the winter in your compost pile. Then, it can come back with a vengeance to haunt your garden in later years.

If you burn the plant, the disease will be destroyed, and you can mix the ash into your compost pile for future years (or use the ash as a liming agent to increase your soil pH).

wood ash
One benefit of burning diseased plants is that you can use the ash as fertilizer or lime in your garden.


Now you have an idea of just how many bacterial, viral, and environmental threats there are to tomato plants. Hopefully, taking some of the preventative measures listed here will help to prevent black spots on your tomato plants.

I hope you found this article helpful – if so, please share it with someone who can use the information.

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Jon M

Hi, I'm Jon. Let's solve your gardening problems, spend more time growing, and get the best harvest every year!

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