Food Gardening Network

Growing Good Food at Home

Dealing with Apple Diseases

Fruit infected by apple scab

Fruit infected by apple scab

Like all food crops, apple trees are susceptible to various fungal diseases. Your best weapons against these are best planting practices, which help prevent disease in the first place.

This is especially important, as there are no fungicides approved for home use for many diseases.

These best practices are aimed at producing strong, healthy trees that can withstand disease, and at avoiding situations that contribute to the development of disease. They involve keeping plants clean, dry, and undamaged.

Watering: Water your apple trees deeply about once every 10 days (check the soil for dryness). Do not over-water; apple trees hate having wet feet! Soggy soil invites disease.

Mulch: Mulch can help with water retention—but be vigilant and check for insect or fungal activity. Do not let mulch pile up around the base of the trunk except when insulating the tree for the winter.

Other best practices include:

  • Buy healthy, disease-free plants from reputable sources
  • Plant your tree in full sun
  • Plant in sites with good drainage; if planting in open ground, choose a higher spot for better drainage
  • Proper winterization
  • Harvest frequently and remove infected fruit, leaves, and branches
  • Prune regularly, at least while the tree is dormant

Common apple diseases

Here are some of the usual culprits that might infect your apple tree. This is not a comprehensive list of all diseases that affect apples, but it’s a good representative sampling. Remember, it’s important to remove diseased fruit, flowers, leaves, and branches to prevent the spread of disease once it’s found its way onto your tree. If your apple trees display other symptoms you can’t link to the diseases listed here and the pest infestations described in the pest section, contact your local extension center for a more specific diagnosis. When you go to choose trees to grow, try to pick the most disease-resistant cultivars available—especially trees resistant to apple scab.

Apple Scab

Cause: Fungal infection that overwinters in fallen leaves and pruning debris

  • velvety spots form on leaves, turning from green to black
  • young leaves wither and drop from branches
  • fruit has distinct, rough, olive-green spots
  • some fruit is misshapen
  • fruit cracks; drops from tree

How it Spreads:

  • fungus survives over the winter in dead wood and leaf litter
  • proliferates in cool, wet weather


  • apply fungicide throughout the growing season
  • prune and dispose of diseased material


  • remove and destroy all infected/fallen leaves
  • spray at bud emergence and after petal fall
  • plant scab-resistant trees
  • disinfect gardening tools before using them on trees


Cause: Fungus

  • leaves turn yellow at the tips, eventually turning brown all around
  • browned, dying leaves
  • dark, sunken lesions on fruit and/or stems

How it Spreads:

  • spores spread by rain, splashing water
  • wind


  • remove all infected parts
  • clear ground of leaf and twig litter
  • apply liquid copper fungicide to reduce recurrence


  • prune tree to provide good air circulation and access to sunlight
  • provide proper water and fertilizer

Bitter Rot

Cause: Fungus that overwinters in mummified fruit, diseased limbs

  • small, brown sunken spots on apples; sometimes look like a target
  • spots rot fruit to the core and eventually mummify the fruit

How it Spreads:

  • splashing water (rain, irrigation) disturbs and disperses spores
  • prefers warm, wet weather


  • destroy infected plant material immediately
  • remove damaged, dead, and diseased limbs


  • liquid copper fungicide
  • plant disease-resistant varieties
  • prune to increase air flow through trees
  • check trees daily

Black Rot and Frog-Eye Leaf Spot

Cause: Fungus
Symptoms on Fruit:

  • red flecks on young fruit that turn into purple pimples
  • irregular black spots with a red halo on mature fruit
  • concentric rings of alternating black and brown
  • lesions remain firm
  • fruit mummifies while still on the tree
  • early fruit fall shortly after petal fall, with no surface symptoms

Symptoms on Foliage:

  • small purple flecks on leaves shortly after petal fall
  • lesions grow with tan/brown centers and purple margins, resembling frog eyes
  • defoliation with heavy infection

Symptoms on Limbs:

  • red-brown sunken cankers

How it Spreads:

  • splashing water (rain, irrigation) disturbs and disperses spores
  • prefers warm, wet weather


  • removed infected plant material


  • liquid copper fungicide
  • prune trees to improve light and air circulation
  • remove damaged, dead, and diseased limbs

Cedar Apple Rust

Cause: fungus spread from cedar/juniper trees

  • small, light yellow spots on upper leaf surfaces
  • spots grow, turn orange with black specks
  • fungal spikes develop on underside of leaves
  • orange gel-like galls appear on cedar/juniper trees in spring

How it Spreads:

  • Fungus spreads to apple trees from cedar/juniper trees in the spring. In dry weather, spores transfer back to cedar/juniper trees, where they overwinter in the tree galls. Infection requires the presence of both apple trees and cedar/juniper trees for infection to spread.


  • neem oil
  • remove and destroy infected plant matter


  • remove cedar/juniper trees from area if possible
  • plant rust-resistant apple cultivars

Crown Gall

Cause: Bacterial infection of root system

  • trees seem stunted, slow-growing
  • smaller than normal leaves
  • little or no fruit on mature trees
  • woody, tumor-like growths develop at ground level and below, restricting the flow of water and nutrients
  • tree death

How it Spreads:

  • bacterium in the soil infects damaged roots
  • gardening tools carrying bacterium


  • fire blight spray


  • disinfect gardening tools
  • take care not to injure tree’s root system

Fire Blight

Cause: Highly contagious bacterial infection
Symptoms on Flowers:

  • withered blossoms and fruit spurs appear to be scorched by fire

Symptoms on Foliage:

  • leaves turn dark brown or black as disease advances
  • branch tips curl into a “shepherd’s hook” shape
  • dieback of twigs and branches

Symptoms on Bark:

  • cankers with orange bacterial ooze

How it Spreads:

  • wind
  • splashing rain or irrigation
  • birds
  • insects
  • flourishes in cool to warm wet weather
  • infects tree at points of injury or damage from insects or weather


  • cut back infected branches 6 to 8 inches below visible signs of infection
  • fire blight spray
  • copper fungicide


  • purchase trees from reputable sources
  • disinfect pruning shears between cuts to avoid spreading infection; use alcohol wipes or a 10% solution of bleach water
  • dispose of or destroy all pruning debris
  • remove and dispose of all mummified fruits and leaves left on the tree in the fall

Powdery Mildew

Cause: Fungus overwinters in buds and emerges in warm, humid weather

  • infected buds open up to four days later than non-infected buds
  • infected buds are covered in spores
  • white, powdery patches on branches, buds, and leaves
  • leaves may curl and turn upward
  • new shoots appear stunted
  • older infections look like a tan or reddish-brown felt covering; these contain spores
  • heavy mildew infections can stunt a plant’s growth and cause early leaf-fall
  • flowers of infected buds do not develop normally and do not produce fruit

How it Spreads:

  • fungus overwinters in buds
  • spores do not need moisture to germinate; often called a “dry weather disease”
  • wind, insects, birds


  • in the spring, prune any shoots that have a white coating (spores)
  • removed and destroy infected areas
  • spray tree with fungicide early in spring, before buds blossom


  • liquid copper fungicide
  • if necessary, sulfur-based fungicide
  • plant disease-resistant varieties
  • remove plant debris

Root Rot (Crown Rot, Collar Rot)

Root Rot: infection of the root system
Crown Rot: infection of the lower trunk and base of roots
Collar Rot: infection above the tree union
Cause: Fungal infection of the soil

  • dark patches of hardened bark on the tree trunk
  • oozing spots on infected areas of the tree trunk
  • dry, cracked bark
  • dark canker on the bark
  • yellowing, dying leaves
  • delayed budding

How it Spreads:

  • phytophthora fungus lives in soil; spreads after heavy rain or irrigation


  • remove and destroy all infected leaves and damaged fruit
  • prune lower branches for better clearance from the ground
  • spray tree with fungicide
  • if tree trunk is not completely wrapped in infection, remove soil from base of tree and scrape off the discolored area to let it air dry


  • plant tree in an area with good drainage
  • keep ground under tree clear of litter
  • choose trees grafted onto rootstock M9

Sooty Blotch and Flyspeck

Cause: Infection of several fungal pathogens

  • green smudges and/or tiny black dots on apple skin; usually appear together
  • symptoms appear early—two to three weeks after petal fall
  • damage is mostly superficial; infected spots can be cleaned off

How it Spreads:

  • fungus survives on infected twigs
  • spores spread by wind, dew, and splashing water (rain, irrigation)
  • fungal pathogens thrive in cool, wet weather, mostly summer and early fall, but also early spring


  • liquid copper fungicide
  • collect and dispose of fallen/infected leaves and fruit to prevent the spread of new spores


  • spray tree with liquid copper fungicide
  • fruit tree spray

Which diseases have you had to treat on your apple trees? Please tell us how you prevent and handle diseases. If you spot other symptoms on your apple trees that are not mentioned here, contact your local extension center or garden center for a consult—and please let us know what you discover.


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