Black Stems On Tomatoes: Treating Tomato Stem Diseases In The Garden

Black Stems On Tomatoes: Treating Tomato Stem Diseases In The Garden

By: Amy Grant

One day your tomato plants are hale and hearty and the next day they’re riddled with black spots on the stems of the tomato plants. What causes black stems on tomatoes? If your tomato plant has black stems, don’t panic; it’s more than likely the result of a fungal tomato stem disease that can easily be treated with a fungicide.

Help, the Stem is Turning Black on My Tomatoes!

There are a number of fungal diseases that result in a stem turning black on tomatoes. Amongst these is Alternaria stem canker, which is caused by the fungus Alternaria alternata. This fungus either already lives in the soil or spores have landed on the tomato plant when infected old tomato debris has been disturbed. Brown to black lesions develop at the soil line. These cankers eventually enlarge, resulting in the death of the plant. In the case of Alternaria stem canker, unfortunately, there is no treatment. However, Alternaria resistant varieties of tomatoes are available.

Bacterial canker is another tomato stem disease that causes black spots on stems of tomato plants. It is readily apparent on older plants as brown streaking and dark lesions. The lesions can appear anywhere on the plant. The bacteria Clavibacter michiganensis is the culprit here and it survives indefinitely in plant tissue. To prevent infection, sanitize equipment with a bleach solution and soak seeds in 130 degree F. (54 C.) water for 25 minutes prior to planting. Till areas of the garden where tomatoes have been grown thoroughly to break up and hasten the decaying of old plants.

Black stems on tomatoes may also be the result of Early blight. Alternaria solani is the fungus responsible for this disease and is spread in cool, humid weather, often after a period of rain. This fungus thrives in soil where infected tomatoes, potatoes or nightshades have grown. Symptoms include small black to brown spots under a half inch (1.5 cm.) wide. They can be on leaves or fruit, but more commonly on stems. In this case, a topical application of copper fungicide or Bacillus subtilis should clear the infection up. In the future, practice crop rotation.

Late blight is another fungal disease that thrives in humid climates. It usually appears in the early summer when humidity is up, with a humidity of 90% and temps around 60-78 degrees F. (15-25 C.). Within 10 hours of these conditions, purple-brown to black lesions begin to dot leaves and spread down into the stems. Fungicides are helpful to manage the spread of this disease and use resistant plants whenever possible.

Preventing Tomato Stem Diseases

If your tomato plant has black stems, it may be too late or a simple fungal application may remedy the issue. Ideally, the best plan is to plant resistant tomatoes, practice crop rotation, sanitize all equipment, and avoid overcrowding to prevent disease from infiltrating your tomatoes.

Also, removing the lower branches and leaving the stem bare up to the first set of flowers can be helpful, then mulch around the plant after removing the foliage to this point. Mulching can act as a barrier as can removing the lower leaves so rain splashed spores cannot infect the plant. Additionally, water in the morning to give the foliage time to dry and remove any diseased leaves immediately.

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The initial symptom, wilting of the whole plant, is usually noticed when the first lot of fruit is ripe and ready for harvest. The wilting is caused by the pith (centre of the stem) disintegrating. This disease is similar to pith necrosis in that respect. Unlike pith necrosis however, the outside of the stem will also become wet and slimy if a tomato plant is infected with stem rot. Sometimes, in severe cases, plant extremities may also turn black and drop off.

An effective treatment has not yet been identified. If you catch it early however, you may be able to prune off affected areas to prevent spread to the rest of the plant. If you do this, disinfect the cut with an infusion of garlic or chives in water. The success of this method is variable.

Cause Of Black Seeds In Tomato

While the natural color of the seeds inside of a ripe healthy tomato from a common variety is a greenish-yellow, there are times when you’ll notice darker seeds when you slice up the fruit.

The causes for why some seeds in a tomato fruit turn black or brown can be multiple. However, if the tomato fruit doesn’t have visible signs of disease, decay, a bad smell, or other unpleasant characteristics, it can be consumed in the majority of the cases.

Below are the most common reasons why some of the seeds can turn dark inside a tomato, even though the fruit looks very healthy.


Most of the time, when you find dark seeds inside a tomato that has no signs of disease, it means that the fruit is overripe.

Maybe you have noticed that the seeds inside a watermelon turn darker when the fruit gets riper. Similar to a watermelon, when a tomato is too ripe, some of its seeds will start turning black.

Depending on how overripe the tomato fruit is, you’ll find fewer or more black or brown seeds inside it.

The seeds’ darker color indicates they are ready to germinate. In rare cases, that even happens inside the fruit.

Before the ripe period, the fruit contains a higher level of a plant hormone called Abscisic acid. One of the functions of this hormone is to prevent seed germination inside the fruit.

When the tomato is overripe, the level of this acid drops, and the seeds may begin sprouting. That and because the tomato fruit contains a high moisture level which creates the proper environment for this process to commence.

Tomatoes Picked Too Early

Not always the tomato fruits that contain dark-colored seeds are overripe. That also occurs in tomatoes who were picked up too early or who fell from the plant for one reason or another.

When you harvest a tomato too early (when it’s still green) and you let it on the window’s sill a few weeks to ripe, its seeds or a part of them might turn black or get a darker color.

I don’t know the exact scientific explanation behind this, but it may again have something to do with the dropping of the level of Abscisic acid since the fruits are detached from the plant for so much time.

Blossom End Rot

Blossom end rot (or BER on short) is one of the most common tomato diseases.

Researchers found that the triggering factors for the occurrence of the blossom end rot diseases on tomatoes and other plants are the impossibility of the plant to take calcium from the soil at a fast enough rate to keep up with the growth or an irregular watering schedule.

You can easily identify this condition by the dark area that appears at the bottom of the fruit, where the blossom originally was.

As an effect of the blossom end rot, you may often find black seeds inside the tomato fruit.

I couldn’t find any scientific study on whether the tomatoes affected by blossom end rot can be 100% safely consumed. Yet, I ate plenty of tomatoes affected by BER for years and I never got sick because of that.

I normally remove the affected areas and what’s left of the tomato fruit doesn’t have an unpleasant look, taste, or smell, I consume it both raw or cooked.

However, that’s only my personal opinion and even though there are countless other similar comments of people who consume them posted on Quora and forums, I wouldn’t say that’s 100% safe for all people (especially for those with many allergies).

Until it is scientifically proven that there are no harmful pathogens left after you remove the affected parts, I’d say to consume them based on your own judgment.

Meanwhile, I also found this article posted by Jessica Strickland on N.C. Cooperative Extension, Wayne County Center which likewise supports the fact that the healthy parts are edible.

Unknown Causes

It is not uncommon to find only one or two black seeds in a perfectly healthy tomato. If the possible reasons mentioned above cannot apply, it might just be a natural cause.

The circumstances which led to the blackened of these may not entirely be known. Probably those seeds simply failed to receive enough nutrients to form a healthy seed or were still young when the fruit stopped growing.

Common Problems When Growing Black Cherry Tomatoes

Statistics show that 95% of American gardeners have tomatoes in their garden. This number would be a perfect 100% if the other 5% had tasted a homegrown tomato.

Anyone who has tasted homegrown tomato fruits and compared them to store-bought will tell you how much you are missing out. The flavor profile is vastly different, and so is the feeling when you are feasting on either.

Even better, when you grow your own, you decide what pesticides and fertilizers to use on your plants.

Still, growing a cherry tomato plant can be frustrating. They might not set fruit or they might ripen and get unsightly and spongy black spots on the bottom.

And that’s not all. Tomato plants might look healthy one night, only to be a skeleton of themselves the next morning. Often, this happens when there is frost.

Which makes identifying common tomato plant problems a must-have skill for any gardener.

The heirloom tomato black cherry withstands more than the regular plant. Yet, they are still vulnerable to common tomato problems.

Some of these problems include:

Blossom-End Rot

Extreme moisture levels prevent plants from absorbing enough calcium from the soil. When this happens, fruits start rotting from the bottom up.

Other triggers of this condition include soil with high acidity or too much nitrogen. To prevent blossom end rot, test your soil pH and nitrogen levels.

A simple preventative measure is to mulch your plant to help the soil retain enough moisture.

Flower Drop

Flower drop occurs when blossoms fall off the plant without the fruits developing. Which is why this condition is also known as blossom drop. One of the biggest causes of blossom drop is a change in temperature.

When night temperatures go lower than 55 or higher than 75 degrees F, plants lose their flowers.

Insects, water deprivation, lack of pollination, and lack of or too much nitrogen also cause blossom drop.

Obviously, you can’t change the weather. What you can do is strengthen your plant by adding fertilizer or organic pesticides such as neem oil. You can also plant milkweed and cosmos to draw pollinators.

Steps to take to prevent problems on tomato stems

  • Plant healthy, disease-free plants.
  • Stake plants to allow good air circulation to stems.
  • Water at the base of plants. Overhead water spreads disease easily.
  • Water in the morning or midday to minimize the amount of time leaves are wet.
  • Monitor plants daily to check for pests.
  • Avoid working on plants when leaves are wet.
  • Remove and destroy affected plants at the end of the season.
  • Solarize soil at the end of the season to destroy soil-borne fungi and bacteria.
  • Rotate crops each year.

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Answer: Blossom End Rot

Blossom End Rot usually occurs earlier in the season, due to up and down temperatures, poor plant establishment, wet spring, and tapers off as the season progresses and plants become better rooted and weather adjusts. It is a physical problem, not a disease, so the ripened fruits can be eaten, just slice off the black spot if desired.

What factors contribute to blossom end rot on tomatoes?

This common problem on tomatoes (also occurs on peppers, squash, melons, cucumbers, eggplant, etc.), and can be the result of many factors:

  • Water stress caused by uneven soil moisture available to the plant. When plants take up moisture from the soil it goes to the foliage first, then to the fruits. The lack of even moisture affects the fruit first resulting in less calcium carried to the fruit.
  • Lack of calcium in the soil available for the plant to take up.
  • Root damages can cause this as well.
  • High feedings of Nitrogen
  • High salt levels in the soil
  • Too low or too high pH
  • Cold air and soil temperatures
  • Soils high in salts.
  • Individual plants are not doing their job internally resulting in BER.

How to Control Blossom End Rot

  • Try adding calcium to the soil and til in, using lime or gypsum, before planting the plants in the ground or containers. These can also be added (top-dress and light raking) once Blossom End Rot shows up on the fruit, to help correct future fruit from being affected. (Calcium Nitrate, Water-soluble lime, hydrated lime, very fine lime become available quickest of the lime – apply early). It may not help if other factors are involved.
  • Establish good soil moisture by increasing timely waterings. Apply mulch to tomatoes to retain soil moisture will help.
  • Do not overfeed the plants, in particular with high nitrogen fertilizer. Excessive growth, stimulated by the high Nitrogen, increases foliage production, which increases the need for water and calcium to the leaves, and results in the lack of moisture and calcium to the fruits. Use an all-purpose garden food, which is lower in N and higher in Potassium and phosphorus, as well as other needed nutrients, including Calcium.
  • Check pH levels. –
  • Cold temperatures (soil and air) will also affect the flow of calcium/water to the plant and fruit. Another good reason to not plant tomatoes too early in the season! Plant when the temperatures get warmer.
  • Keep records as some selections are more susceptible than others.

For container gardening potting mixes, that do not contain calcium it is harder to keep evenly moist, etc. It is advised to calcium to the mix using Soil Moist to help keep even moisture levels. The larger the pot, the less watering is needed.

Temporary solutions are Blossom End Rot sprays and crushed Tums or Rolaids. You are better off correcting the overall situation causing the problem.

6 Plus Reasons Why Your Tomato Plants Are Wilting

Recently Transplanted Seedlings

The first reason that might cause tomato wilting is if you recently transplanted your tomato plants, especially if the first day was sunny. Too much sun after transplanting into your garden beds causes sun-stress to plants that aren’t sufficiently hardened off before going out.

Root damage during transplanting might also cause wilting. Secondary roots break easily when transplanting tomato plants out of their seedling pots, and a smaller root-ball leads to less capture area for water to get into the plant.

Don’t worry if root damage is the problem, you’ll notice an improvement within a week or two.

Watering Improperly

The most common reason why your tomato plants are wilting is due to either a lack of water or an abundance of water. Tomato plants need two inches of water per week, either through manual watering or rainfall. Providing over or under this amount for extended periods will lead to wilting.

How do you know if you’re over or underwatering? Here is what to consider.


Tomato plants need between one to two inches of water each week to stay sufficiently hydrated. During warmer weather, their water needs increase to the two inches mark.

The first thing you should do is to check the soil. If it’s dry one to two inches below the soil’s surface, it’s time to water.

Here’s what else you might notice if you aren’t providing enough watering.

  • Drooping
  • Thin, dry, paper-like leaves


Plants also wilt and droop if there is too much water in the soil. You can take a look at the ground to help you understand whether or not you’re overwatering. If the soil is wet to the touch an inch or two below the surface, it needs to dry out watch the plant and wait for the ground to become dry below two inches below the surface.

Here’s what to look for when determining if you’re overwatering your tomato plants.

  • Yellow leaves that start at the oldest leaves.
  • Drooping leaves
  • Leaves won’t feel dry or paperlike because they’re hydrated.

Fungal Diseases

If your tomato plants are correctly waterly and start to wilt more after ensuring the appropriate amount of water is provided, your plants might have fungal wilt. There are three common types of wilting fungal diseases in tomato plants.

Verticillium Wilt Fungus

Verticillium wilt is a fungal disease that doesn’t usually kill a plant, but it does cause growth reduction and production. It thrives in cool, moist environments, appearing most often towards the middle or end of the growing season.

This fungal disease causes v-shaped yellow discolorations on the plant’s lower leaves before spreading throughout the leaves. If the leaves aren’t droopy in the evenings, chances are it’s not verticillium wilt.

Verticillium wilt lives in the soil and stays alive for years. If you discover your plants have this, it’s best to rotate crops to avoid planting tomatoes in the same area.

Fusarium Wilt Fungus

Fusarium Wilt is a soil-borne fungal disease that enters the vascular system of the plant through its roots. Like most fungi, Fusarium Wilt likes to spread in warm, moist, humid areas.

As this fungus spreads throughout the vascular system of your plant, it clogs the system, preventing the flower of water from reaching the rest of your plant.

Over time, this leads to symptoms like yellowing leaves, stunted growth, and wilting. In most situations, the lower leaves start to turn yellow, and often one side develops problems before the entire plant.

Unfortunately, destroying the infected plant is the only option. There are no treatments for this fungus.

Southern Blight

At the start of this disease, it can be hard to distinguish from fusarium or verticillium wilt, but Southern Blight quickly shows its differences. This fungal wilt causes an appearance of white mold on the soil around the tomato plant’s base. It also might cause rapid wilting of the plant.

In the late stages, Southern Blight causes the entire plant to collapse.

As you can see, both of these wilting fungal diseases are similar. They cause the plant to wilt and die quickly because the fungus clogs the plant’s vascular system. The easiest to identify is Southern Blight, but that doesn’t mean it’s better to have that type.

The worse part of having tomato fungal wilt diseases is that they are all untreatable and nearly impossible to control. If you determine that your plants have this disease, it’s essential to remove them entirely from your garden and avoid planting any nightshade vegetables in the same soil for two to three years.

Tomato Spotted Wilt Virus

Are your tomato plants wilting and have purple or brown spots on the leaves? Chances are your tomato plants have a virus called Tomato Spotted Wilt Virus.

Unlike other viruses and diseases, Spotted Wilt affects the tips of the plants which are actively growing. It can affect fruit, causing ring-shaped marks to develop. It either causes the tips of the plant to wilt or die back in extreme cases.

Some other symptoms of Tomato Spotted Wilt Virus include:

  • Leaves turning brown or bronze.
  • Leaf curling

Tomato Spotted Wilt Virus’s problem is that there are no treatments, and removing the plants is a crucial step. The virus will spread to the other plants nearby if not removed.

Avoid planting tomatoes in the same spot for at least one to two years. It’s important to note that even though it’s named Tomato Spotted Wilt Virus, it doesn’t affect only tomato plants. Various plants experience this virus, spreading by different thrips species that feed on the plants’ sap.

Tomato Bacterial Wilt

While it’s less common, some tomato plants wilt due to Tomato Bacterial Wilt. It can be hard to identify this disease until the plants are dead because wilt is the only predominant symptom. You won’t notice discoloration of leaves or anything else. The plant continues to stay green even as the plant wilts until death.

Tomato Bacterial Wilt causes the plants to wilt and die quickly. After death, close inspection shows that the stem’s inside is dark, watery, and hollow.

Bacterial wilt is common in areas with hot, humid conditions, and it thrives in soil with a high pH range. Like other tomato problems, Bacterial Wilt affects the plant through the vascular system, and it lives in the ground for years.

There is no way to treat or fix Tomato Bacterial Wilt, and removing the plants is the only step possible. If you suspect that your plant has this bacteria, solarizing the garden bed can prevent it from spreading to future plants the disease survives for years in the soil or weeds. It can be hard to get rid of this bacteria from a garden bed even if left unused for years.

Less Common Reasons for Tomato Plants Wilting

If you still suspect something else is wrong with your tomato plants, causing them to wilt, here are some of the less common reasons for tomato plants wilting.

Stalk Borers

Stalk borers are pests that attack a wide variety of plants, including tomatoes. The larvae dig into the stems and tunnel throughout them. The entrance hole is small and hard to locate, so discovering them that way is nearly impossible.

You can identify stalk borers if you find cream and purple striped caterpillars crawling on your plants.

Since treating stalk borers is challenging due to not noticing their presence until it’s too late, most affected plants wilt and die. The safest course of action is to pull out the plants and destroy them, which might kill the stalk borers as well.

Root-Knot Nematodes

While far from the most common pests, nematodes arguably are one of the most damaging tomato plants. Nematodes spread around your garden, naked to the eye under the surface, feeding on tomato roots.

As their name indicates, root-knot nematodes damage roots, causing knots and balls that make it impossible for the roots to take up water and nutrients throughout the plant. This causes the plant to wilt in hot conditions, but it might make a slight recovery in the evenings.

There is no cure or way to stop nematodes. By the time you realize there is a problem, the damage is done. If root-knot nematodes are common in your region, consider growing resistant varieties that are marked by the letter N.


Aphids are a common pest on tomato plants, and most infestations are minor, requiring little aid from you. These tiny pests like to suck out the sap from your plants as they spread a sticky substance over the leaves called honeydew.

That’s where the problem begins. Honeydew also attracts ants, which can cause a significant problem for your plants. It also attracts sooty mold that causes a black film to develop over your plants.

Like other pests, aphids damage your plants in vast quantities, leaving them vulnerable to bacteria, pests, and viruses that might cause even more severe damage.

Planting Near Allelopathic Plants

Certain plants are called allelopathic plants because they produce a substance that makes it harder for other plants to grow nearby. Typical examples are sunflowers, butternut trees, and black walnut trees.

The most common one is walnut toxicity because black walnut trees produce juglone, a toxic material that kills solanaceous crops, such as tomatoes, potatoes, peppers, and eggplant. Walnut toxicity causes:

  • Stunted growth
  • Yellowing leaves
  • Wilting of foliage
  • Death of the plants

Finding the Cause of Tomato Plants Wilting

The hardest part of dealing with your tomato plants wilting is figuring out what the cause is. Some reasons for tomato wilting are fixable, but many of the fungus, bacteria, and viruses that lead to wilting equal death to your plants. The most important thing you can do is to pay close attention and catch wilting as soon as it appears.



Joey G Smith says

I live in Mississippi and the last 6 years I have plated better boy tomatoes. They have done well the first 4 years, but the last 2 years they have wilted just as they have gotten loaded with large green fruit. I was able to prevent spread to about 1/3 of crop by pulling out the diseased plants. I believe this to be some kind of wilt virus. I only have this area that is ideal for tomatoes because of trees, etc. in the remainder of my yard. Is there any way to treat the soil prior to planting to kill the virus. I had thought about spaying bleach over the soil and mixing it in with a tiller. What say you??

Watch the video: How To Stake, Prune And Tie Tomatoes - Single Stem Pruning Method