A reader recently reached out to me and asked if I knew anything about apple trees getting black leaves. I knew a bit about it, but I wanted to provide them with the best answer I could. So, I did some research. Here’s what I found.

Apple trees get black leaves from diseases including black rot, apple scab, and fire blight. While fire blight is a bacterial disease, black rot and scab are fungal. All three diseases are highly contagious and difficult to get rid of, with the best method being prevention. Pruning and sprays may help.

So, while apple trees get black leaves from several causes, how can we tell which issue is causing it, and how can we fix it? Let’s take a closer look.

1. Black Rot

black rot disease on an apple tree
Black rot disease, causing frog-eye leaf spot and mummified fruit.

Black rot is a fungal disease Diplodia seriata (also named Botryosphaeria obtusa) that causes black lesions on leaves, fruit, and branches on apple and pear trees. This disease most commonly survives winters in branch cankers and infected fruit and begins spreading during wet weather.

Apple trees that are already stressed are more likely to be infected by black rot. Here are some common reasons why apple trees get stressed and contract black rot:

  • Winter injury
  • Drought
  • Waterlogged soil
  • Excess fertilizer
  • Infections from other diseases, such as fire blight

Trees infected by fire blight often later develop black rot. Fireblight results in dead wood that is easily infected by the black rot fungus.

Michelle Grabowski, University of Minnesota Extension

How to Identify Black Rot

LocationBlack Rot Symptoms
LeavesCircular spots with purplish/reddish edges and tan interiors. Also called “frog-eye leaf spot”.
FruitLarge brown/black rotten areas (sometimes at the core), small black spots on older infections, firm flesh, occasionally dry out while attached to the tree
FlowersLarge brown rotten areas
BranchesCankers (reddish/brown sunken areas usually with rough or cracked bark). More difficult to see than leaf or fruit infections.

You can most commonly see black rot on the apple tree’s leaves and fruit, but can sometimes be seen on flowers and branches. Typically, branches are most vulnerable on the frost-side or at points where they meet the trunk as they’re the last to harden off before the winter.

How to Treat Black Rot

The best ways to prevent and treat black rot are by pruning the diseased branches and fruit, and best practices such as proper watering and fertilizer. You can also plant black-rot-resistant apple varieties. Fungicides and other sprays are not recommended for this disease.

Prune all dead or diseased branches and dried and shriveled fruits as these are common sites of infection and allow the disease to survive the winter. The best time to prune is in the winter, when temperatures are freezing (below 32ºF) as the fungus is dormant. February and early March are the best months.

After pruning the dead and diseased branches, prune the tree to shape it.

If you’re not pruning in freezing weather, make sure the shears are cleaned with vinegar or bleach (both are equally effective) in between cuts.

To prevent the disease from spreading from the pruned branches and fruit, it’s recommended to burn or bury them. Any apple trees that are cut down should have their stumps removed as they can spread black rot spores.

Avoid pruning leaves that are infected with black rot as the leaf’s spots don’t release spores and don’t seriously affect the tree’s health (source). Pruning leaves can actually cause more harm as it affects the tree’s ability to photosynthesize and fight off the disease.

Fungicides are not recommended as cultural practices are the most effective and should be attempted first. Certain sprays can be used to prevent leaf spot and fruit rot, but will not prevent infection of the branches.

Black Rot Resistant Apple Trees

One of the best ways to prevent black rot in the first place is to select and plant varieties that are resistant to it. Best gardening practices such as proper watering, sunlight, airflow, and fertilizer are still necessary for the optimal chances of preventing this disease.

Apple Tree VarietySusceptibility to Black Rot
ArletModerately susceptible
BraeburnLess susceptible
CameoModerately susceptible
CrestonLess susceptible
EnterpriseLess susceptible
FortuneModerately susceptible
FujiLess susceptible
Gala SupremeLess susceptible
Ginger GoldModerately susceptible
Golden DeliciousLess susceptible
Golden SupremeModerately susceptible
Goldrush Less susceptible
HoneycrispModerately susceptible
NY75414Moderately susceptible
OrinVery susceptible
PioneerMacModerately susceptible
PristineVery susceptible
SansaModerately susceptible
SeshuModerately susceptible
ShizukaModerately susceptible
SuncrispModerately susceptible
SunriseVery susceptible
YtakaModerately susceptible
Source: Ontario Ministry of Agriculture, Food, and Rural Affairs (OMAFRA)

2. Apple Scab (Also Called Black Spot)

apple scab with black spots on leaves

Apple Scab (Venturia inaequalis) is the most common disease apples, pears, and crabapple trees contract. This fungal disease primarily affects the leaves and fruit, but can also infect shoots, buds, and blossoms. Heavily infected leaves turn yellow and then brown and black as the spots grow.

These spores mainly survive and spread from diseased leaves that dropped over the winter.

Scab is most common in the warm, rainy season as water and wind allow the spores to spread. In these conditions, infections can take place as soon as 9 to 17 days. Once the infection takes hold, the fungi shoot more spores into the air. As long as the leaves are wet enough, this reproductive process will repeat.

Leaves that are infected typically drop by mid-summer. Infection over multiple seasons can weaken and kill the apple tree.

How to Identify Apple Scab

LocationApple Scab Symptoms
Leaves1/2 inch olive-green round spots. Heavily infected leaves turn yellow, and then brown and black.
FruitOlive-green spots that turn brown. Young fruit become deformed and cracked.

How to Treat Apple Scab

The best way to manage apple scab is to plant naturally resistant trees (source). Some fungicides can help manage this disease if applied at key points of infection.

Here are some best practices to treat and manage apple scab:

  • Clean up infected leaves in the fall (you can burn, bury, or compost them)
  • Prune the tree’s canopy to promote airflow and sunlight, reducing moisture and therefore fungal growth
  • Avoid densely planting apple trees. Keep a spacing of at least the size of a mature tree’s canopy
  • Avoid fungicides on resistant or immune varieties or those already infected. Trees already infected with Apple scab will not benefit from fungicides until the following spring. Fungicides don’t cure the tree but protect new leaves from getting infected.
  • If using fungicides, apply when green leaf tips emerge, about 1/2 inch
  • Keep in mind that fungicides that are labeled organic can still be toxic

Scab Resistant Apple Trees

Again, the best way to prevent and manage apple scab is to plant resistant or immune trees. Here’s a table I put together to help show the best (and worst) varieties when it comes to apple scab.

Apple Tree VarietySusceptibility to Apple Scab
Pixie CrunchImmune
William’s PrideImmune
BeaconLikely To Be Infected
FiresideLikely To Be Infected
HaralsonLikely To Be Infected
KeepsakeLikely To Be Infected
Paul RedLikely To Be Infected
Sweet SixteenLikely To Be Infected
WealthyLikely To Be Infected
Chestnut CrabLikely To Be Infected
CortlandVery Likely To Be Infected
HoneygoldVery Likely To Be Infected
McIntoshVery Likely To Be Infected
State FairVery Likely To Be Infected
ZestarVery Likely To Be Infected
Source: University of Minnesota Extension

3. Fire Blight

fire blight black and brown leaves on a pear tree

Fire blight (Erwinia amylovora) is a highly infectious bacterial disease that affects members of the rose family—including apple, pear, crabapple, rose, cotoneaster, mountain ash, hawthorn, quince, spirea, and pyracantha. Fire blight causes browning, blackening, and disfiguring of the leaves and fruit, sometimes killing the tree.

This disease spreads most often in the springtime when it’s warm and wet, spreading the fastest when the temperature is above 70ºF (source). However, during the winter, fire blight is dormant. This is why providing preventative treatment to the trees during the winter is important in handling this disease.

The bad news is fire blight is the most common apple tree disease, and there is no cure for it (source).

The good news is some treatments prevent and slow the spread of fire blight. With these practices, fire blight is manageable and should have little to no further impact on your trees.

How to Identify Fire Blight

LocationFire Blight Symptoms
LeavesWilt, turn grey-green before turning brown or black, sometimes appear scorched by fire (hence the name). Remain on the tree into winter.
FruitTurns dark and shriveled, does not drop right away—stays attached to the branch for months.
FlowersDroop or shrivel, then turn brown or black. Remain on tree into winter. Flower infections are rare if blooming in cooler temperatures.
BranchesCankers appear, sunken and darker. Cracking, peeling, and brown staining of sapwood are likely. Light-yellow or cream-colored infected sap oozes.

How to Treat Fire Blight

There are no known trees that are immune to fire blight. However, some varieties can limit or slow the disease—giving you time to prune the diseased branches (more on these varieties below).

Here are some best practices to treat and manage fire blight:

  • Prune in late winter when the tree and bacteria are dormant
  • If pruning in other seasons, disinfect pruning shears with vinegar or bleach (both are equally effective) between each cut
  • Prune at least 8 inches below the site of infection/canker (cutting into 8 inches of healthy wood)
  • Burn or bury infected cuttings (unlike fungal diseases, it’s not recommended to compost infected cuttings of fire blight. This is likely because compost is bacteria-based and could allow fire blight bacteria to survive).
  • Avoid over-pruning as it can weaken the tree. The goal is to first prune any diseased branches, and second to prune for shape—promoting airflow and sunlight to lessen the bacterial spread
  • Avoid chemical fertilizers high in nitrogen as this can quickly feed the fire blight bacteria. Opt for a slow-release fertilizer with a balanced NPK, or compost.
  • Chemical sprays are not recommended unless fire blight is an annual issue. They’re completely ineffective against branch cankers/infections
  • If fire blight reaches the main trunk, the tree cannot be cured and removal is likely best to prevent other trees from getting infected

To see an active map of fire blight infections in the US, check out this map on uspest.org.

Also, to read more about this disease, feel free to visit my other post: Fire Blight Treatment: Non-Organic & Organic Solutions.

Fire Blight Resistant Apple Trees

Apple Tree VarietySusceptibility to Fire Blight
BeaconLeast Resistant
FiresideLeast Resistant
HoneygoldLeast Resistant
PaularedLeast Resistant
WealthyLeast Resistant
CortlandLess Resistant
KeepsakeLess Resistant
McIntoshLess Resistant
State FairLess Resistant
Sweet SixteenLess Resistant
HoneycrispSomewhat Resistant
ZestarSomewhat Resistant
HaralsonMost Resistant
LibertyMost Resistant
Red BaronMost Resistant
SnowSweetMost Resistant
Source: University of Minnesota Extension

Sprays and Fungicides

Even though I lightly touched on sprays and fungicides, I wanted to provide you with more information in case you’re interested in pursuing them. Here are the most effective sprays for the above diseases and their pros and cons (keep in mind that sprays were not recommended for black rot and fire blight).

Chemical Fungicides

Some copper fungicides are effective in dealing with certain apple tree diseases (such as apple scab). When applying copper fungicides, all parts of the tree should be covered in the spray and used until runoff. Instructions vary depending on the product, so refer to the label for more specific information.

While chemical sprays can be useful at times, many have been discontinued due to safety issues or ruled as ineffective. Because of this, many gardeners are looking for other, more natural options.

So, if copper sprays aren’t the safest organic solution, what are some safer (and still effective) organic solutions?

Organic Sprays

Vinegar Spray

While organic solutions typically get a bad rep for not being as effective as chemicals, there are many anecdotes of them working for many organic orchard farmers. For example:

Alice and Dale Bautz of Great Falls report successfully using white vinegar to treat their fire blight-infected apple tree in 2010 at their former home in Dickinson, N.D… Bautz said they doused it before, during and after the blossom times, and paid particular attention to any wounds left from pruning.

Great Falls Tribune

If you’re interested in using vinegar to treat apple tree diseases, I found a solution that’s been shown to work:

  1. Add 6 cups of water and 4 cups of white vinegar to a 1-gallon garden sprayer
  2. Spray the tree from top to bottom (including the trunk, branches, leaves, blossoms, and fruit)
  3. Repeat again in 2 weeks


Remember to prune any infected branches before applying the vinegar solution. This will greatly reduce the spread of disease.

Essential Oil Spray

Research from Washington State University has shown that oregano, thyme, and cinnamon essential oils are a viable treatment for fire blight. Use a spray of 23% thyme oil or 60% cinnamon oil a few times per year.

Even though I use peppermint essential oil in my homemade toothpaste, I have a hard time accepting other uses for them—especially when it comes to treatments. However, new research from Washington State University shows that using essential oils to treat fire blight has shown promising results.

Essential oils (e.g. from thyme, mint, cinnamon, oregano) have known antimicrobial activity. In one laboratory study active compounds from Origanum compactum (oregano family) and Thymus vulgaris (Thyme) were most effective (Kokoskova et al., 2011). In another study, Apium graveolens (celery seed) and Curcuma longa (turmeric) essential oils showed a reduction in Erwinia amylovora (fire blight) virulence (Akhlaghi et al.). These oils are rich in antioxidative phenolic compounds which are believed to be responsible for their antimicrobial activity (Chizzola et al., 2008).

S.Tianna DuPont, WSU Extension Specialist, Assistant Professor. Washington State University Extension.

In case you missed it, here are the essential oils that are recommended to treat fire blight:

  • Oregano
  • Thyme
  • Celery Seed
  • Turmeric
  • Cinnamon

If you’re interested in recreating the promising solutions used in the studies, here are the measurements and directions that I was able to gather:

  1. Use a 23% solution of Thyme oil or 60% Cinnamon oil
  2. Apply when flowers reach 80% bloom, 1 day after 100% bloom, and when the petals start to fall

It’s important to hit most diseases with a solution before the blossoms open, as blooming is when the tree is at its most vulnerable. Additionally, sprays after bloom and during petal fall are also recommended.

And this isn’t only for small orchards either. Essential oil sprays such as Thymegard, Thymox, and Cinnerate are available to commercial growers.

For more information on using essential oils to treat fire blight and other apple tree diseases, refer to the resource linked above.

Other Organic Sprays

Most other organic sprays contain citric acidic, which reportedly has mixed results. These sprays can also be easily washed off in the rain. However, after they remain on the leaves for at least 3 hours, it can help prevent and treat pear tree diseases.

Neem oil (made from the neem tree) is also a popular spray to reduce and eliminate pests, bacteria, and some fungal infections (including apple scab).

If you do decide to opt for a spray, remember that trees should be sprayed when they’re dormant and at the first sign of budding.

Final Thoughts

Even though chemical sprays are an easy way out, like all easy and convenient things, there are usually long-term costs. Namely to the plants, soil, and surrounding beneficial life. Before using conventional sprays, weigh the pros and cons and consider using organic or permaculture-based treatments first.

Along with the above sprays, here are some of the most effective organic methods that I’ve found to manage black leaves on apple trees and other plant diseases:

  • Minimize tree stress (use best practices such as only watering when the soil is dry and providing compost and mulch)
  • Use a homemade whey spray
  • Use the STUN method

If you’re interested, I’m adding two videos below so you can learn more about organically managing diseases on fruit trees.

Homemade Whey Spray

Stefan Sobkowiak – The Permaculture Orchard has a great video on a safe, homemade, and most importantly—effective fungicide (hint: the secret ingredient is whey).

STUN Method

Mark Shepard, on his 100+ acre farm, uses a method called STUN (sheer total utter neglect) and it works wonders for him. He uses no chemical fertilizers, sprays, or any other dependencies. Through the struggle, his fruit trees become stronger and his job gets easier. In a way, it’s survival of the fittest.

Check out the below video for more about Mark Shepard and STUN.


Similar Posts