Pepper Plants Getting Black Spots (Are They Dead Or …?)

If you are seeing black spots on your peppers, you are probably concerned – and wondering why it is happening. It turns out that the location of the black spots can help you to determine what is causing the problem.

So, why are your pepper plants getting black spots? Black spots on the fruit itself can be caused by blossom end rot, sunscald, anthracnose, or wet rot. Black spots on the leaves can be caused by black sooty mold, fusarium, bacterial leaf spot, or tobacco mosaic virus. Black spots on the stems can be caused by phytophthora blight or sclerotinia.

Let’s look at each of these causes in a little more detail, along with symptoms and treatments. Then, we’ll talk about how to do everything you can to prevent diseases in your pepper plants in the future.

Let’s get started.

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Why Are Your Pepper Plants Getting Black Spots On The Fruit?

If your pepper plant has black spots on the fruit itself, then start here to determine the probable cause.

long red bell peppers
Peppers should be red, orange, yellow, green, or even purple, but not black!

Blossom End Rot

Blossom end rot causes a dark, leathery spot to appear on the bottom or low on the side of a pepper.  The spot starts off tan, and then turns brown and black. The spot may also become leathery or sunken-in.

pepper blossom end rot
Peppers can get blossom end rot, just like tomatoes. This is often due to uneven watering.

Blossom end rot spots can become infected by soft rot bacteria or other pathogens.

Blossom end rot usually starts at the first fruit set, and the problem also affects the fruit of others in the nightshade family (such as tomatoes and eggplants).

Blossom end rot is caused by calcium deficiency in the pepper plant. However, this calcium deficiency could be due to any of the following reasons:

  • Lack of calcium in soil
  • pH imbalance in soil
  • Uneven watering (too much, too little, or both in combination)
  • Excessive magnesium in soil
  • Excessive ammonia fertilizer, or too much nitrogen (for more information, check out my article on low-nitrogen fertilizers).

Remember that you should not treat affected plants with Epsom salt (magnesium sulfate), since it contains no calcium at all. In fact, the magnesium can make the problem worse by competing with calcium for uptake by the plant’s roots.

Instead, make sure that your pepper plants have water when they need it – don’t let the soil dry out too much. Feel the soil with your hands a few inches deep to see if it is dry enough to water.

hose spray nozzle
Water your peppers when they need it – feel the soil with your fingers at a depth of a few inches to tell.

For more information, check out this article from the University of Georgia on blossom end rot in peppers.


Sunscald first appears as white, tan, or yellow blisters on the fruit, usually on the side of the plant that gets the most sun. The fruit may also crack, and you will eventually see black mold growing on the sunscald patch, which explains the black spots you see.

pepper plant
Don’t prune away too many pepper leaves at the top of the plant, or the fruit can get sunscald.

Generally, sunscald occurs on the sides of the fruit (rather than on the bottom, as in blossom end rot).  Sunscald can also affect tomatoes.

Sunscald damage makes pepper fruit more susceptible to diseases.

There is nothing you can do to change the amount of sunlight you get in your garden. However, when sunlight is intense, use row covers to protect exposed fruit from the sun’s harshest rays at midday.

row cover
Use row covers or shade cloth to protect pepper fruit from intense sunlight.

Another possibility is to use shade cloth to shield plants from the sun.

For more information, check out this article from Missouri Botanical Garden about sunscald in peppers.


Anthracnose is caused by the fungus Colletotrichum – different types can infect the fruit at different stages (mature or immature).

Anthracnose causes large brown or black lesions on pepper fruit. These lesions can appear anywhere on the fruit.

Eventually, you will pink spores growing in the lesions. These spores can be spread by rain, and they can survive the winter in soil or compost.

(Be careful about the disease spreading – anthracnose can also affect tomatoes and other plants!)

There is not much you can do to cure a fungal infection once it has taken hold of your pepper plant. Remove and destroy an infected plant and its fruit.

Do not compost the material, since anthracnose can survive over the winter in a compost pile.

For more information, check out this article from Ohio State University on Anthracnose in peppers.

Wet Rot

Wet rot in peppers is caused by the fungus Choanephora cucurbitarum. It typically occurs in moist, humid regions.

It first appears on flowers that are still connected to fruit. Then, the disease spreads to the fruit itself.

Dark gray or black growth of the fungus will appear on fruit, and the fruit itself may also rot and turn black.

Wet rot can also affect eggplant and other crops. For more information, check out this article from Seminis on wet rot.

Other Causes

In some cases, black spots on fruit can also be caused by cucumber mosaic virus or Phytophthora (more on this later).

Why Are Your Pepper Plants Getting Black Spots On The Leaves?

If your pepper plant has black spots on the leaves, then see the causes below to find out what may be causing the problem.

Black Sooty Mold

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

Sooty mold is caused by fungi that grow in tiny threads that eventually become thick enough to see.

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

Black sooty mold is caused indirectly by aphids. When aphids feed on peppers (or other plants), they suck the juices out of the leaves and stems.

Aphids feed on plants and secrete honeydew, which feeds the growth of black sooty mold.

After they digest the juices, aphids leave behind a sticky and sweet waste product, called honeydew. The black sooty mold then grows and feeds on this honeydew and gives pepper leaves or stems a black appearance.

To prevent black sooty mold from affecting your pepper 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.


According to Wikipedia, fusarium is a wilt fungal disease, caused by fusarium oxysporum. Fusarium can cause wilting, chlorosis (yellow, discolored leaves), necrosis (blackening and death of plant tissue), leaf drop, and stunted growth.

You will often see the tips and edges of older, lower leaves turning yellow, brown, or black first. This normally occurs later in the growing season.

You may also notice that only one side of a pepper plant is affected. Fusarium can infect tomatoes and other plants as well.

Fusarium prefers warm temperatures and moist soil, and it can survive for a long time in compost. If you see any infected plants, destroy them – and do not use the material in your compost pile.

compost bin
If a pepper plant is infected with fusarium, do not put in in your compost pile, since the disease can survive a long time in compost.

Your best bets to prevent the disease are to plant resistant varieties and practice crop rotation. Look in the plant descriptions in your seed catalog and look for the code “F” for fusarium resistance.

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

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Bacterial Leaf Spot

Bacterial leaf spot causes symptoms that vary depending on leaf age (location). It can also affect the stems of pepper plants.

Older leaves (lower on the pepper plant) will develop small “pimples”. Younger leaves (higher on the pepper plant) will develop water-soaked spots.

bacterial leaf spot pepper
Bacterial leaf spot causes pepper leaves to turn yellow or brown and then fall off.

The pimples and spots later become tan or gray in the middle, with darker black edges. In warm, humid weather, the spots can get bigger.

Unlike sooty mold, these spots cannot be washed or scraped away without harming the plant, since the bacteria has infected the leaf tissues.

The leaves of infected plants may turn yellow or brown, and then fall off. This lack of leaves can also cause sunscald on the pepper fruit, as mentioned earlier.

Bacterial leaf spot can be spread by rain or watering infected plants. This disease can also affect tomatoes.

Rain or water splashing can spread bacterial leaf spot between plants.

Bacterial leaf spot can also survive from one season to the next in seeds and plant debris.

There is no treatment, so remove and destroy infected plants, and do not compost the waste material. Use crop rotation, and avoid planting tomatoes and/or peppers in the same location in your garden every year.

For more information, check out this article from the University of Maryland on bacterial leaf spot.

Tobacco Mosaic Virus

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

The disease can survive for weeks or months on infected material.

Infected plants should be removed and destroyed. Avoid working with your plants after touching or using tobacco products.

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

Why Are Your Pepper Plants Getting Black Spots On The Stems?

If your pepper plants are getting black spots on the stems, then these are a few of the possible causes you should look into.

Phytophthora Blight

Phytophthora blight is caused by the oomycete phytophthora capsici. In addition to affecting stems, it can cause the roots and fruit of peppers to rot.

Phytophthora is a devastating disease that can cause the loss of an entire crop. It can also affect tomatoes, eggplant, and other crops.

Pepper plants infected with phytophthora will display black lesions on their stems. In addition, fruit and leaves will wilt, but stay attached to the plant.

The fruit may eventually collapse due to rot, and the disease may spread to other plants by rain or watering. The disease may re-infect neighboring plants several times during one growing season.

The spores can overwinter in soil and have the potential to survive for up to 10 years.

To prevent phytophthora, choose pepper varieties that are resistant to the disease. Be careful not to splash water on leaves when watering, and plant peppers far enough apart to prevent easy transmission of disease.  lso, be sure to use crop rotation to discourage the disease.

For more information, check out this article from the University of Massachusetts on phytophthora blight.


According to Wikipedia, sclerotinia sclerotiorium is a plant fungus that can cause a disease called white mold under proper conditions. Sclerotinia first causes pale to dark brown or black lesions on the stem at soil level.

The white mold later grows to cover these necrotic brown lesions. Afterward, symptoms spread up the plant, including chlorosis, wilting, leaf drop, and eventual death. The fruit can develop lesions if it comes in contact with the soil.

Sclerotinia can infect over 400 plant species. It can spread quickly from plants of the same type or different types.

To prevent the spread of sclerotinia, be sure to plant in well-drained soil and leave enough space between plants. Also, use crop rotation in three or four year cycles to discourage the disease.

Avoid using too much nitrogen fertilizer, which promotes dense green growth (leaves) and provides an infection route for this disease.

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

How Can You Prevent Peppers From Getting Diseases?

There are a few ways to prevent peppers from developing these problems in the first place.

Plant Disease Resistant Pepper Varieties

First, choose pepper plants that are resistant to diseases that are common in your area. Usually, the seed company or garden center selling the seeds or seedlings will indicate disease resistant in the plant description.

seed package
Before you buy pepper seeds, check the catalog for disease resistance of each variety.

For example, an “F” in a seed catalog description often indicates resistance to fusarium wilt.

Use Crop Rotation

Make sure not to plant the same crop in the same part of your garden every year. Instead, switch plants every two, three, or four years to avoid the spread of disease.

Note that tomatoes, peppers, and eggplants are all in the nightshade family. As such, they share some of the same diseases.

So, try to avoid planting these crops in the same place for multiple years in a row. Rotate nightshade plants with other crops, such as legumes (peas, beans, etc.).

pea plant
Rotate planting nightshades (like peppers) with legumes (like peas).

As an added bonus, a crop rotation practice helps to prevent nutrient depletion in the soil.

Water Plants Close To The Ground

When you water your plants, water them more deeply and less frequently, to encourage the development of stronger root systems.

Also, water during the day, not late in the evening when the leaves and roots are more likely to stay wet for a longer time. Otherwise, you risk root rot or fungal diseases on leaves.

Consider using a drip irrigation system to ensure enough water for pepper plants without overdoing it.

drip irrigation emitter
Drip irrigation provides enough water to plants without splashing water and spreading disease.

Also, consider the possibility that you may be over watering your plants. For more information, check out my article on over watering your plants.

Remove Infected Plants

If you notice any infected plants, your best bet is to remove them to prevent further spread of the diseases. Destroy the plants instead of composting them, since diseases can often survive in soil or compost for a year or longer.


Now you have a better idea of what might be causing black spots on your pepper plants. Remember that the location of the spots is one of the keys to identifying the cause.

Once you figure out a probable cause, it is time to take action to rid your garden of the problem.

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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