Tomato Stems Turning Black – Causes and Solutions

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Last Updated: April 7, 2023

Tomatoes are notorious for disease, pest, and environmental issues. You’ll often find leaves curling in the mid-summer heat, yellow leaves from poor nutrients, and even tomato stems turning black.

More often than not, black spots on tomato stems is caused by disease. The exact bacteria or virus to blame can be hard to identify. So in this article, I’ll go through a few common reasons that tomato stems turn black, and what you can do to fix it.

Black spots on tomato stem - Tomato blight

Why are my tomato stems turning black?

No matter where you live, your tomato plants are not immune to diseases! Most of the reasons for black spots on tomato stems and leaves are some form of disease.

But don’t be discouraged! It is much more rare to have a completely disease-free tomato plant than one with some disease. The good news is that many diseases can be controlled, and still allow for some edible harvests.

Tomato diseases that cause black stems:

  • Alternaria stem canker. More common along the coastline of California, alternaria stem canker is not very common in the home garden. Stems, leaves and fruits will have brown or black lesions with concentric rings. Over time, the spots will grow, eventually killing the plant.
  • Early blight. Early blight is very common in the Northeast. Infected plants will have small black spots on stems, leaves, and fruits. These spots are usually sunken and sometimes have concentric rings. Avoid watering over the tops of your plants, and space them properly for good airflow.
Tomato blight on leaves and stem - black spots on tomato plant
Appearance of early blight on tomato leaf and stems.
  • Late blight. Late blight usually comes later in the season, and has a much different appearance to early blight. Brown leaves quickly spread to create large patches of brown or black stems and leaves. This disease can cause catastrophic losses in susceptible tomato varieties. High humidity and mild temperatures create the perfect environment for the fungus to infect plants. Planting late blight resistant cultivars can help reduce the chances of infection.
  • Bacterial speck. This disease causes black stems on tomato plants, especially where branches meet with stems (petioles, see picture). Bacterial speck is most common in cool, wet conditions, so avoid transplanting outdoors too early in the season.
  • Tobacco streak. Symptoms of this disease usually starts with leaves curling downward with brown, dead leaf veins. This can spread to young stems, showing as brown or black streaks along the stems.

While diseases are most likely to blame for black tomato stems, there is one other potential cause:

Should I cut off black stems/stem rot?

When you see black stems, it is tempting to remove it to improve the aesthetic of your garden. However, does it actually help to remove stem rot on tomato plants?

In short, removing diseased foliage and stems can help reduce the spread of disease to other parts of the plant. While removal alone may not stop disease from spreading, it can at least slow it down.

In addition to removing any dead or diseased parts of your tomato plants, you may need to treat them with a fungicide to further reduce the spread. An organic copper-based fungicide can help reduce the spread of diseases such as blight, powdery mildew, and bacterial spot.

If you shy away from using a fungicidal spray, why not try cinnamon? This household spice is a natural fungicide that may help suppress certain fungal infections. Sprinkle cinnamon over the affected plants, stems and fruits in dry weather.

How to avoid tomato plant diseases

While different diseases are caused by different pathogens, many of them can be avoided by following some best practices in the garden:

  • Plant disease-resistant varieties. One of the best defenses against disease comes before you even plant. Seed selection is an invaluable tool that we have, especially in the world of tomatoes. There are countless disease resistant tomato varieties available to choose from. Determine which diseases are most prevalent in your region, and find a few cultivars that are resistant.
  • Bottom prune. Many fungal pathogens survive in soil. This makes the lower foliage of your tomatoes the perfect entry point. By keeping the plants bottom pruned, you help reduce soil splashing onto vulnerable lower leaves. Do this with clean shears and in dry weather to allow the wounds to heal.
  • Mulch your plants. Another defense against soil-borne pathogens is a thick layer of mulch. There are many options for mulch types, but no matter what you use, the barrier will prevent soil from splashing up onto your plants in heavy rainfall.
  • Space plants at least 24″ from each other. Aeration is key to a healthy tomato plant. Overly dense foliage or spacing plants too close together can lead to poor airflow and increased risk of disease.
  • Avoid watering over the leaves. Many pathogens spread via spores that require standing water to reproduce. While rainfall is unavoidable, always water your tomatoes at the base of the plants, not over the leaves.
Watering tomato plant at base
  • Clean up plant debris in the fall. Disease-causing bacteria and fungi overwinter on plant debris and in the soil. Help reduce populations of these pathogens by cleaning up any and all plant debris from your garden before fall.
  • Avoid unnecessary damage to plants. Pruning tomatoes is important, but timing it is just as vital. Never prune in wet or highly humid conditions to reduce the risk of pathogens entering the wounds.

These best practices will help you avoid many other diseases. Black tomato stems are caused by diseases, but other infections can be even more detrimental to overall harvests.

Other tomato stem issues

Black tomato stems are definitely the most striking of the stem-related issues. However, there are some other common tomato stem problems to look out for. Here are a few examples and their causes:

  • White lumps. In high-humidity conditions, or tomato stems will often begin forming new roots along their stems. These are known as ‘adventitious’ roots, and they grow to propagate plants asexually. This is usually nothing to worry about, and the white lumps will typically remain small nubs.
  • Broken stems. Strong winds can easily snap or split tomato branches. These splits can extend and grow more severe over time. In addition, later in the season, heavy fruits can cause plants to droop and break if they aren’t properly supported. Planting tomatoes deep early in the season can help prevent stem breaks, and using tomato cages or stakes can prevent breaking later in the season.
Super sweet 100 cherry tomato climbing stake
Tall tomato attached to a stake for support helps prevent broken stems.
  • Gray or white fuzz. While tomato stems are naturally fuzzy, if the fuzz appears to be patchy or concentrated, it may in fact be mold. There are a number of molds that can infect tomatoes, such as gray mold. This will usually impact stems and leaves, and sometimes fruits that are left on plants for too long.

I hope this article helps you identify the cause of your tomato stems turning black. Hopefully the issue doesn’t cause the end of your tomato plants. Either way, you can be more prepared for next year!

Cherry tomato trusses from Super Sweet 100


Hi, I’m Calvin, creator of Tomato Geek. I have over a decade of gardening experience and I love helping others grow healthy plants!

2 thoughts on “Tomato Stems Turning Black – Causes and Solutions”

  1. I grow my tomatoes in the north of England. Must grow in the greenhouse. I grow in the borders. The tomatoes were badly affected by blight. Would it be safe to grow tomatoes in the borders next year, or should the soil be replaced?

    • If it was late blight, you may have more issues with the soil. Few tomato varieties are resistant to late blight (thought there are some). Early blight is more common and removing soil won’t likely keep it out of the greenhouse. My best advice is to find blight-resistant hybrids and grow them. Tomatoes are always prone to disease, so finding a few varieties that hold up against what is in your region is critical!


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