Common Pepper Diseases and How to Prevent Them

Types of pepper plants including Capsicum annuum, C. chinense, C. baccatum, C. frutescens, and C. pubescens are all prone to common diseases usually observed in the Solanaceae family.

Tomatoes and peppers share several diseases, but eggplants, the third fruiting vegetable in the Solanaceae family, are less disease prone. Several of the pepper plant diseases are terminal and require burying crops. Prevention, however, is easy and is strongly advised.

This article covers all the pests, diseases, and physiological disorders common to pepper plants. I have listed the pathogens responsible for the diseases and management suggestions to prevent infestations.

Pepper Plant Fruit Physiological Disorders 

The table below is a summary and is further covered in more detail.

Blossom End Rot:Avoid irrigation fluctuations and excessive ammonia-based fertilizer
Catfacing:Watch for very low temperatures during pepper plant blossoming or get a variety resistant to the deformity.
Cracks:Manage irrigation consistency, especially in hot weather. Keep an adequate balance between fruit and foliage. Cracks can be caused by too little foliage from pruning.
Rain Checks:Also called micro-cracks, and can be prevented by maintaining healthy foliage and selecting varieties with good foliage cover. Triggered by high humidity.
Sunscald:Keep an adequate balance between fruit and foliage – it can be caused by too little foliage from pruning.
Zipper Scars:More common in greenhouses. 

Pests Common to Pepper Plants

The pests listed in the table below serve as a reference. These pests spread several pepper plant diseases, specifically an aphid infestation.

Cucumber BeetlesCorn borers
Flea BeetlesCutworms
Fruit FliesFruitworms
Stink Bugs

Diseases, Pathogens, and Abbreviated Prevention Methods

The table below provides a list of all the 

AnthracnoseColletotrichum gloeosporioides and C. acutatumThe most common pepper plant problem.
Use disease-free seeds and transplants.
Seed hygiene
Rotate to non-Solanaceous crops for 3-4 years.
Ensure proper drainage, soil temperatures, and airflow.
Reduce splashing
Promptly rogue finished crops
Bacterial CankerClavibacter michiganensis subsp. michiganensisCrop rotation
Choose seeds and seedlings from a reputable supplier
Avoid wetting leaves
Ensure adequate air flowRogue plants at the end of the season
Bacterial SpeckPseudomonas syringae pv.General hygiene
Avoid working with wet plants
Keep foliage dry
Bacterial SpotXanthomonas campestris pv.vesicatoriaPlant pathogen-free seed or transplants
Seed hygiene
Keep leaves dry
Don’t work with wet plants
General tool hygiene
Damping-off seed and seedling rotVarious pathogens, incl. Pythium, Phytophthora, Rhizoctonia or FusariumGeneral hygiene
Use warmer water (68 -77 °F (20 – 25 °C))
Improve drainage
Early BlightAlternaria solaniPlant disease-resistant varieties.
Maintain plant vigor.
Remove volunteer weeds.
Rotate to non-Solanaceous crops for 3-4 years.
Fusarium WiltFusarium oxysporum f. sp. lycopersiciPlant resistant varieties
Rotate to non-Solanaceous crops for 3-4 years.
Use raised beds, replacing soil if needed.
Gray MoldBotrytis cinereaEnsure airflow
Plant hygiene
Work only with dry plants
Maintain adequate, consistent soil moisture
Late BlightPhytophthora infestansWhere possible, plant-resistant varieties
Plant early in the season to escape high disease pressure later in the season
Keep foliage dry
Scout plants often, removing infected plants, fruit, volunteers, and weeds
Leaf BlightSeptoria lycopersiciPlant pathogen-free seed or transplants
Seed hygiene
Keep leaves dry
Don’t work with wet plants
General tool hygiene
Leaf MoldPassalora fulvaAvoid getting foliage wet – use drip irrigation
Improve air movement between rows and individual plants.
Lift plants.
General tool and stake hygiene – sterilize with alcohol or 10% bleach solution.
Remove crop residue at the end of the season.
Burn it or bury it away from tomato production areas.
Powdery MildewLeveillula tauricaAvoid fields with a history of the disease.
Rotate to non-Solanaceous crops for 2 to 3 years.
Improve airflow by using stakes
Avoid wet foliage
Promptly destroy finished crops
Southern BlightAthelia rolfsii (synonym for Sclerotium rolfsii)Manage aphid populations
Use sweet corn as border plants
Manage weeds
Neem oil disrupts the spread of aphids
VirusesCucumber mosaic virus (CMC); Tobacco mosaic virus (TMV); Potato virus (PVY); Pepper mild mottle virus (PeMV); Tomato spotted wilt virus (TSWV)Manage aphid populations
Use sweet corn as border plants
Manage weeds
Neem oil disrupts the spread by aphids
White Mold (Timber Rot, Drop, Stem Rot)Sclerotinia sclerotiorum, S. minor, and S. trifoliorumStart with clean soilSanitize tools and equipment
Destroy (burn) infected crops and weeds.
Weed management
Wilt Verticillium albo-atrumSelect disease-resistant varieties.
Rotate to non-Solanaceous crops for 2 to 3 years.
Consider soil solarization
Destroy infected plants
Sanitize tools and equipment
Consider earlier crops to alleviate heat pressures
Use mulch from resistant trees
Control weeds

Growing Healthy Pepper Plants

Of all the crops, peppers are the most closely associated with different cultures. The most common pepper species grown is Capsicum annuum, which includes sweet green peppers, colored bell peppers, as well as other sweet and hot peppers, including banana, jalapeño, Hungarian wax, Italian, and serrano. 

The other cultivated species include much hotter peppers that can rate above 1,000,000 on the Scoville scale, a measure of the pepper’s pungency. Pepper plants grow a moderate 3 feet tall (91 cm)—plant transplants into your pepper garden about two weeks after the average last frost date.

Your pepper crop is less cold tolerant than tomatoes, so delay transplanting until soil (at a depth of 4 inches (10 cm)) has warmed to 60 °F (15 °C). Plant pepper seedlings 18 to 24 inches (45 to 60 cm) apart in rows at least 18 inches (45 cm) apart. 

Spacing within a wide row can be 12 by 12 inches (30 x 30 cm). Pepper plants will produce all summer with perhaps a short break for the hottest weather, so repeat plantings aren’t required. 

Harvest peppers (especially bell peppers) while still green and immature whenever they reach a usable size. Harvest Hot peppers, except jalapenos, are picked when fully ripe. 

All peppers will change color as they ripen to yellow, orange, red, or purple. Peppers are noticeably sweeter when mature, generally taking two to three months after planting. 

Handle peppers and chiles with care, as the stems can be brittle, needing to be cut off rather than plucked. You can expect a yield of as many as 80 fruits per 10-foot row (3 m).

Don’t plant your peppers and chiles too early. You can grow your pepper plants from seeds started indoors or purchase transplants. 

Peppers offer a wide variety of shapes, colors, and levels of hotness, and identifying different seedlings can be a challenge, so either mark your trays (if you’re growing from seeds) or use a reputable seedling supplier that keeps track of the different varieties. 

Unless you live in a tropical climate, pepper seeds are rarely planted directly into the garden. Start pepper seeds indoors, planting them about half-an-inch deep (13 mm) four to six weeks before the average last frost date. 

Optimal germination rates will be achieved in 75 to 80 °F (24 – 27 °C) warm soil, with seedlings appearing in about a week. The preferred outdoor soil temperature should be between 65 and 80 °F (15 and 27 °C). 

Transplant into larger pots as the seedlings grow, giving them good light so the plants stay short and stocky. If you want to play with light colors, blue light encourages plants to develop more compact. 

Young pepper plants will not tolerate prolonged periods below 50 °F (10 °C) and do not grow well in cool or wet soil. 

Common Disease Prevention Strategies for Pepper Plants

The table above shows that good crop management strategies can prevent several pathogens affecting pepper plants.

Ensure Good Soil Drainage

Most soil-borne pathogens emerge in anaerobic conditions. Healthy soil (as opposed to dirt) is a product of soil biodiversity, hosting diverse populations of aerobic microorganisms (bacteria, fungi, actinomycetes).

Any addition of compost is not as much about adding carbon matter as it is about adding food (carbon) for these microbes. The microbes are responsible for making plant nutrients available to plants.

Soil microbes (and macrofauna) boost soil water management capacity, improving drainage while ensuring water retention for plant hydration.  

Indicators of Healthy Soil

  • The soil surface is medium to dark brown.
  • The soil is sufficiently deep and loose to support healthy root growth.
  • A hole 2-3 feet deep can be dug without much effort.
  • Macrofauna, like earthworms, beetles, ants, and centipedes, is evident in the top six inches.
  • When soil is wet, it crumbles. After a significant downpour, soil aggregates (small clumps or crumbs) keep their structure.
  • Hours after a rainstorm, water does not remain on top of the ground, and there’s limited erosion.

A pepper plant needs constantly damp soil. I cover the best way to further water your pepper plant – for now, ensure your garden drains well.

Testing Your Soil’s Drainage

  • Create a hole that is 12 inches in diameter and 12 inches deep.
  • Add water to it. Refill the hole with water the following day.
  • Within eight hours, all the water ought to drain out.
  • The soil is very sandy if it drains more than four inches of water every hour. A speed of less than an inch per hour is considered slow-draining and may signify high clay content, soil compaction, a high-water table, or a constrictive sediment layer (caliche).

Ensure Good Air Circulation 

Though not often considered, airflow is vital to plant health and development. As leaves transpire, they create a gaseous cocoon around themselves. Plants rely on air movement to remove their transpiration, especially when relative humidity levels are high. 

When plants are planted too close to each other, light and airflow are compromised and can impede plant growth. Poor air circulation compromises evaporation rates, and the growing humid conditions can promote the spread of fungi and their associated diseases.

In calm air surroundings, plant leaves are surrounded by a very thin layer, the boundary layer. There is a correlation between the boundary layer thickness, gas rate, and leaf energy exchange. 

A thicker boundary layer reduces the amount of heat, carbon dioxide, or water vapor a leaf may lose during transpiration or respiration. 

Boundary layer thickness is influenced by leaf size, leaf texture, pubescence, and the density of the foliage. 

Environmentally, wind speed has the most influence on boundary layer thickness. Without airflow, boundary layers thick enough to impede photosynthesis may form.

Make sure your pepper plants are not too close to each other and that air can move through them to minimize a build-up of the humidity pathogens love.

Avoid Wetting Pepper Plant Leaves

Pepper plants, unlike tomatoes, are shallow-rooted. Whereas a tomato plant’s roots grow to a depth of between 12 and 18 inches (30 – 45 cm), the roots of a pepper plant only grow to 6 to 12 inches deep (15 to 30 cm).

Soil water is subject to three forces:

  • Gravitational pull
  • The soil’s cation exchange capacity
  • Capillary action

Due to the Earth’s gravitational force, deeper roots can access water for longer periods. Shallow roots depend on effective aggregates, high cation exchange levels, and regular watering to remain hydrated.

While adding compost to boost the soil’s biota is critical to meeting the first two requirements, i.e., improved aggregates and CEC, you will still need to water more regularly (without overwatering).

The easiest way to ensure your plant has consistent access to water is to fill a 50-gallon drum and use a small solar pump to drip irrigate your beds. A 10 x 4-foot bed needs 25 gallons a week if you water the average inch weekly.

Drip irrigation is the best way to water pepper plants as the foliage remains dry, preventing common pepper plant problems. Water helps pathogens spread, and keeping leaves dry is critical for all plants producing fruit (peppers, tomatoes, eggplants, and okra). 

Heat Treatment for Pepper Seeds

Dipping seeds in hot water can help eliminate pathogens in and on seeds, preventing their presence in your crops. The suggested water temperature averages 122⁰F (50⁰C), and immersion times average 25 minutes but vary according to the crop. 

Most purchased seeds are pre-treated with Thiram 75 WP, a seed-protectant fungicide. Never eat bought seeds, and if you treat them with hot water, dispose of their water responsibly. The Ohio State University Extension has an exciting factsheet on the topic.

Use this technique for all the pepper plant diseases in the table above, where I reference seed hygiene as a possible management strategy.

Grow Pepper Plants in Raised Beds

Starting with a healthy, raised bed is the best way to keep your pepper plants healthy. Optimal pepper plant health (applies to all vegetables) can be achieved by following the directions below.

Creating a Raised Bed

Start by adding 4 to 6 inches of compost where the beds will be. Vegetable beds should be about 40 square feet (3.6 m2), four by 10 feet or 1.2 by 3 meters. 

If you add 6 inches (15 cm) of compost, every 54 square feet (5 m2) of garden bed will require a cubic yard (0.76 m3) of compost. However, if you only add four inches (12 cm), a cubic yard of compost will cover 81 square feet (7.5 m2) of the garden bed. 

Mix the compost into the tilled soil and the soil from the paths to create raised beds. If you have turf, cover the beds with cardboard sheets and cover these with a 50/50 compost/soil mix. By the time the cardboard decomposes, the grass will have suffocated and died.

Even if you plan to make your compost on-site, you may need to buy some or get some as contributions when you start. 

If you’re prepared to make your garden a demonstration site to stimulate local home composting, the municipality may discount some compost through its composting program. 

Commercial mushroom production waste compost (mushroom compost) and worm castings are excellent alternatives. To ensure you get quality compost, look for the US Composting Council’s Seal of Testing Assurance while shopping (STA). 

Raised beds can be placed with plants, bricks, bales, or various materials. It is not essential to contain them, and not doing so increases the raised bed’s capacity to drain, improves access to plants, and warm up.

Culling Infected Plants

Fungi spores are incredibly light and can be blown for several miles in the wind. It is advised that infected plants are buried, but I always burn mine to prevent potentially infecting the soil.

If you have a closed composting bin, all pathogens mentioned above will be eliminated in the higher temperatures of traditional aerobic composting. 

How to Identify the 20 Pepper Plant Diseases 

Anthracnose caused by Colletotrichum gloeosporioides and C. acutatum 

The most frequent sign is lesions on pepper fruit. The lesions start tiny, round, and depressed, increasing in size to form mats of salmon to pink-colored spores as the condition worsens.  

Lesions’ cores might be anything from tan to orange to brown or black. This disease is distinguished by the colored spore mats that may be observed on the pepper fruit. 

Concentric circles frequently surround the lesions. The entire pepper fruit will eventually decay. Anthracnose can result in a latent infection where signs of the disease may only appear on ripening fruit.

Bacterial Canker caused by Clavibacter michiganensis subsp. michiganensis

Wilting is the main sign that your pepper plant may have bacterial Canker. On older plants, wilting may begin with the lower leaves or the leaves on one side and progress to the entire pepper plant.

On young plants, bacterial Canker will cause the entire will to wilt with vascular discoloration visible in cut stems. Infected leaves may develop yellow borders. 

Spots on leaves and fruit are the result of secondary diseases. Pepper fruit develops white dots with a black center. Bacterial Canker infects flowers or the base of trichomes (hairs on leaves and stems).

Bacterial Speck caused by Pseudomonas syringae pv.

Bacterial Speck manifests as dark brown to black lesions of varied sizes and shapes on pepper fruit and stems. At first, the tissue around the lesions is yellow.

Large-scale marginal tissue death (necrosis) is typically caused by leaf lesions that are concentrated close to the margins.

Small, slightly elevated lesions on immature pepper fruit range in size from microscopic specks to 0.125 inches (3 mm) in diameter, and they generate raised black dots on mature fruit.

Fruit lesions are typically superficial, rarely going deeper than a few cells.

Bacterial Spot caused by Xanthomonas campestris pv. vesicatoria

Premature leaf drop from infected pepper plants exposes fruit to the sun, causing sunburn.

Fruit lesions start as little, slightly elevated blisters that turn into dark brown, scab-like lesions as they grow in size.

Eliminating or reducing the number of pathogens that can cause disease is the first step in any disease control plan. Infected seed is a significant source of the bacteria that causes bacterial leaf spots (BLS) in peppers. 

A crucial BLS control technique is the use of disease-free seeds and transplants. In an efficient BLS management campaign, infected weeds and crop debris must also be controlled as they present additional sources of the disease.

Damping-off seed and seedling rot caused by various pathogens, including Pythium, Phytophthora, Rhizoctonia or Fusarium

True damping-off can be mistaken for plant damage brought on by highly soluble salts, excessive fertilizing, overwatering, and seedling death from extreme heat, cold, or chemical injury. Finding the precise source of damping off requires a laboratory diagnosis.

Young plants with damping-off typically decay at the ground level and topple over. 

Start with a soilless growing medium and avoid contaminating it with dirty hands, tools, or containers to prevent damping off infections. Remove sick plants immediately, irrigate without splashing water, and keep hose ends off the ground.

Early Blight caused by Alternaria solani

Early Blight first manifests as roughly circular brown spots on leaves and stems near the base of afflicted pepper plants. 

Concentric rings form as these spots grow, giving the areas a target-like look. Spots frequently have a yellow halo. 

Eventually, many locations on a single leaf will combine, causing significant leaf tissue loss. Early Blight can cause a pepper plant to lose its lowest leaves and even die completely.

Fusarium Wilt caused by Fusarium oxysporum f. sp. lycopersici

Initially, during the warmest part of the day, plants wilt and then recover at night. Although the yellowing of the leaves varies, it does occur. Individual leaflets or the entire leaflet on one half of a compound leaf will occasionally become yellow on one side of the plant.

The plant quickly wilts and goes yellow, but leaf browning is uncommon. The bottom stem’s vascular tissue is brown and dark crimson when the epidermis (outer tissue layer) is peeled back.

Gray Mold caused in pepper plants by Botrytis cinerea

Young, infected leaves first appear brown with blighted areas, often V-shaped. Abundant gray-brown mycelial growth with conidia appears on dead or dying tissue.

The stems turn white and develop cankers, and the infected stems girdle and wilt. Mycelium spreads from the flowers to the fruit and back toward the stem. Pepper fruits turn light brown or gray and develop a soft rot. The pepper fruits may also develop ghost spots or necrotic flecks surrounded by whitish halos. 

Gray mold is often confused with Sclerotinia white mold.

Late Blight caused in pepper plants by Phytophthora infestans

Pepper plants can contract an infection in any of their above-ground components. Foliar diseases begin as tiny, wet sores that quickly grow and turn pale green. The leaves eventually wither and perish. 

Plants with severe infections may perish. A white mold starts to form on the lesions on the underside of the leaves. Infected green fruit develops brown or olive-colored lesions that can lead to fruit rot and smelly, decaying vines.

Leaf Blight caused in tomato and pepper plants by Septoria lycopersici

The lower plant canopy is typically where Septoria leaf blight is initially noticed, though it can gradually spread to fresh growth. 

Circular lesions with dark edges and tan-brown cores characterize this disease. Under optimal conditions, these lesions can be numerous and cause severe blighting. 

Leaf Mold caused in pepper plants by Passalora fulva

First to be infected are the oldest leaves. On the upper edge of the leaf, tiny pale green-yellow patches (1/4 inch) start to appear and finally turn entirely yellow. 

On the underside of the leaf, opposite the spots, a velvety mold develops as the leaf ages. Blossoms that are infected will turn black and drop off. Leaf mold seldom develops outdoors.

Powdery Mildew caused in several plants by Leveillula taurica   

It might be challenging to find powdery Mildew on pepper. Only the underside of leaves exhibits the typical white powdery development of powdery mildew illnesses, which turns brown rather than staying white.

On the upper surface, diffuse yellow spotting frequently appears. As with bacterial leaf spots, the affected leaves often fall off the plant.

Southern Blight caused by Athelia rolfsii (synonym for Sclerotium rolfsii)

The bottom stem, which is in contact with the ground, is where the most prevalent symptom appears on tomatoes and pepper. Initially, the stem along the soil line normally develops a brown-to-black lesion. 

All parts above ground will suddenly and permanently wilt as the infection spreads quickly and can fully encircle the stem. Around the soil line, young plants could topple over.

White mycelium often forms on stem lesions in damp environments and can occasionally spread several centimeters up the stem of tomato and pepper plants. 

After a few days, the mycelia mat may develop tan to reddish-brown, spherical sclerotia (1 to 2 mm in diameter).

Fruit that comes into contact with infected soil can quickly become infected by the fungus. Lesions will initially appear as sunken, light-yellow regions that eventually become soft, water-soaked spots with star-like patterns. 

The fruit may collapse within three to four days, and the lesion cavity can be filled with white mycelium and sclerotia. In the beginning, rotten fruit does not have an unpleasant smell.

Viruses, including Cucumber mosaic virus (CMC); Tobacco mosaic virus (TMV); Potato virus (PVY); Pepper mild mottle virus (PeMV); Tomato spotted wilt virus (TSWV)

Pepper plants infected with CMV show symptoms that can be transient and frequently manifest as ring-spot or oak-leaf necrotic patterns on lower, mature leaves. On peppers of the determinate variety, ring-spot symptoms are more noticeable.

Whether on the fruit or the foliage, necrotic signs are a shock response linked to an early virus infection. Occasionally, plants next to ring-spotted plants have a mild to moderate mosaic pattern and a generally uninteresting appearance.

White mold, also called timber rot, leaf drop, or stem rot, is caused by Sclerotinia sclerotiorum, S. minor, and S. trifoliorum

Initial infection frequently occurs along the soil line near the stem’s base. Bleached spots and watery soft rots appear on the stems and leaf axils. Subsequently, white cottony mycelium spreads to the stems, leaves, petioles, and flowers.

The plant begins to wilt, and the afflicted tissues bleach and deteriorate. Clumps of mycelium develop into black sclerotia with a white pink inside in 7 to 10 days. Sclerotinia white mold and Botrytis gray mold are frequently confused with each other.

Wilt Verticillium albo-atrum

On chile peppers, the early signs include stunting and a mild yellowing of the lower leaves. Excessive yellowing and leaf shedding could happen as the condition worsens.

The degree of symptom intensity is strongly influenced by nutrient availability and soil and air temperatures. The fungus invades the xylem components and prevents the movement of water.

Variable levels of vascular discoloration may appear as the disease progresses and the plant starts to wilt due to water stress. Before they permanently wilt and die, infected plants may recover for a few days at night.

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