19 Apple Tree Diseases and How to Treat Them

Keeping apple tree diseases in check is a basic part of proper care for your fruit trees. There are dozens of diseases that can attack your apple trees, and they vary from bacterial infections to fungal infections and viruses. Some apple tree diseases will only cause superficial damage, but others can be devastating once they take hold and kill off your trees to lead to a total fruit loss.

Since this can be very expensive to replace, we’re going to outline 19 big apple tree diseases, how to spot them, and how to treat them to save your trees. This will ensure you have everything you need to keep your garden thriving and healthy.

1. Anthracnose Canker and Bull’s-Eye Rot

Anthracnose canker is a very severe apple tree disease that is very common in the United States in the Pacific Northwest region. However, it’s also a problem throughout the world, and you can find it from China to the UK. The Neofabraea fungi is the main cause of this apple tree disease, and they produce cancers that can lead to a fruit infection known as bull’s-eye rot.

The canker phase is the biggest issue with this disease, and it can cause severe damage to your trees. It’s common for commercial growers to have to replace entire orchard blocks to prevent it from spreading. The cankers will mature at the year mark and start producing spores that will infect the apples and lead to bull’s-eye rot.

To treat it, you should prune out the cankers and remove the stems or even an entire tree that has heavy canker infections. If it’s permitted, burn all of the infected foliage and trees to get rid of it. Since it can be hard to see all of the cankers present on a tree, you also want to provide fungicide treatments on your trees.

The spores from these cankers can infect the fruit on the tree at any point after it blooms throughout the entire growing season. To make it even more challenging, the fruit infections on your trees aren’t detectable. You will only see them post-harvest, roughly four to seven months after you put the fruit in storage. When this fungus infects the fruit, it can cause a specific symptom set. N. alba will cause white mycelium with soft rot and N. malicorticis will give you circular, sunken brown lesions. Applying fungicides before the autumn rains, during petal fall, and pre-harvest will help control bull’s-eye rot.

Rose Apples by anslatadams / CC BY-NC-ND 2.0

2. Armillaria Root Rot

Along with being a highly fatal pathogen for a variety of shrubs, trees, and woody vines, this apple tree disease’s claim to fame is that it’s the biggest organism known around the world. Also called the Honey Mushroom, there is a colony in Oregon that spreads over two and a half miles. In Eastern deciduous forests, this pathogen has strong links to root rot.

Since this fungus has such a wide host range, it can be a catastrophic apple tree disease. It works by infesting small pieces of wood in the soil, and this can eventually evolve to infect the apples. Any apples that get infected have reduced terminal shoot growth, and it’s common to see the leaves turn purple during the fall months much earlier than healthy trees do. In midsummer, one huge symptom that is impossible to miss is the collapse of any diseased trees.

It’s common to see mushrooms forming at the base of your infected trees in early fall or late summer. Unfortunately, there is no way to effectively treat this apple tree disease, and prevention is the only way to avoid huge losses in your orchards. As an odd twist, honey mushrooms are safe to eat and delicious.

Armillaria mellea by Charles de Mille-Isles / CC BY 2.0

3. Apple Scab

This very serious fungal apple tree disease is caused by Venturia inaequalis. It will form as small lesions during the spring on the bottom of your leaves. It will eventually spread to the top of the leaves and to the fruit where it shows up as brown scabs. By midsummer, this apple tree disease can cause a total foliage loss, and this makes the tree very vulnerable to other diseases taking hold.

Spraying your trees with fungicide early in the springtime can help prevent this problem, but it’s very difficult to control this fungus. You want to carefully bag up last year’s leaves and fruit to stop it from spreading more. Another option you have is to plant apple tree varieties that are resistant to it, including Williams Pride, Liberty, Pristine, Jonafree, and Enterprise. However, Rome Beauty, Cortland, McIntosh,and  Red Delicious are all prone to developing issues with it.

Apple by Felip1 / CC BY-NC 2.0

4. Bitter Pit

The first symptom that indicates you have this apple tree disease present is water-soaked, small lesions on the fruit. These spots will slowly change to look like bruises, and they’ll sink in. Even though your apples will show symptoms while they’re still on the tree, they won’t get bitter until you harvest them. This is a physiological condition that isn’t due to soil pH. It happens when calcium gets very concentrated in the leaves instead of in the fruit.

Being in a dry and hot planting zone can increase your chances of having issues with this apple tree disease. The leaves transpire much more in this climate, and the calcium slowly diverts to the leaves as a result. Once the fruit develops symptoms, there is nothing you can do. The best thing you can do is to avoid excessive potassium and nitrogen fertilizer use because this encourages your tree to grow more foliage than fruit. Spraying the trees with calcium chloride or calcium nitrate through the summer can help prevent it too.

Image from page 22 of “Bitter-pit of the apple” (1909) by Internet Archive Book Images / CC0 1.0

5. Cedar-Quince Rust

This strange fungus requires a host plant in order to attack the apple trees. For example, maybe you have flowering quince shrubs dotted around your landscape (Chaenomeles speciosa), and they make perfect hosts for this apple tree disease. It will spread from the shrubs to the apple trees if you give it a chance.

The biggest symptom that indicates that this apple tree disease is present is seeing rusty spots on the tree’s leaves. The apples will also be misshapen and have mottling damage. If you routinely grow a plant type that serves as a host, you should also check the host plant and see if they are carrying it. Rust galls are rusty-orange horns that send out spores in the spring to attack the apple trees. You want to get rid of the host plants to prevent it, and you can also grow Redfree, Freedom, or Williams’ Pride apples as they are rust-resistant cultivars.

Cedar Quince Rust 1 by Matthew Fells / CC BY-NC 2.0

6. Chlorosis

A lot of apple tree diseases and insects can cause discoloration on the leaves of the tree, and this condition is called chlorosis. If the yellowing appears throughout the leaves on your tree and it’s not limited to smaller patches, your tree could have an iron deficiency. This physiological issue’s symptoms include yellowing of the leaves and eventual leaf death. One classic hallmark is that the veins stay a green color while the foliage surrounding them turns yellow. This will happen to the younger leaves first, but it can spread to the entire tree.

The problem may also be that your soil doesn’t have an iron deficiency, but it does have a pH level that is too high. This is a problem in soils that are rich in lime like you’ll find in New Mexico. You can add chelated iron to help solve this problem, but this is a very temporary fix. You can also see symptoms that mimic chlorosis from an iron deficiency but the true cause is lower manganese levels. A soil test will help determine which deficiency your tree has. To solve it you can get and use an acid-forming nitrogen-based fertilizer, or you can apply a foliar spray in April of manganese sulfate.

Hoya calycina with Capsicum chlorosis virus by Scot Nelson / CC0 1.0

7. Cork Spot

If the apples look like they have hail or insect damage, you want to take a closer look. There is an apple tree disease called cork spot that produces these symptoms. The spots can eventually progress from small dimples to soft or corky spots that are a half-inch wide. Instead of an organism causing this apple tree disease, it’s the direct result of the pH levels in the soil being far too low. This will eventually lead to a calcium deficiency. This is curable by adding lime to the soil if the pH falls below 6.0. You can also spray your trees with calcium chloride every 10 days until you harvest all of the fruit.

Oak Apple Gall by Colin / CC BY-NC-ND 2.0

8. Crown Gall

This is a very unusual apple tree disease that can affect a broad plant range, and it’s a bacteria at the root cause. You can find this bacteria in soil all over the world, and it’s the Rhizobium rhizogenes bacteria. This bacteria species actually genetically engineers plants in a natural way, and it does so by changing the DNA and causing the plant to produce galls. These are a type of tumor. Wooly apple aphids can also encourage gall production, but you can tell the difference between the two since crown galls don’t get hidden under a cottony, white wax. This apple tree disease is usually fatal with no cure.

Crown Gall by Scot Nelson / CC0 1.0

9. Fire Blight

If your apple tree looks like someone set fire to the tips, you could have a problem with a fire blight bacteria infection. This disease is the worst with new shoots, but it can spread to all parts of your tree that are above the ground very quickly. The weather will dictate how quickly the disease spreads, and humidity or rain can encourage fast spreading. If the temperature is between 75°F and 85°F, it can be particularly severe.

When these conditions all come together, you want to stop overhead irrigation. If you’re using it, try to reduce how much moisture lands and stays on the foliage. Pruning the tree can go a long way toward controlling this apple tree disease. You can carefully spray it with copper to treat it, but too much copper can cause the bacteria to gain a resistance or damage your fruit.

Fire blight of apple caused by Erwinia amylovora by Scot Nelson / CC0 1.0

10. Flat Apple Disease

You can find the virus that causes this disease in British Columbia and in the western portion of the United States. The virus is called CRLV or the Cherry Rasp Leaf Virus. However, there are concerns that this apple tree disease could spread to growing regions in the northeastern portion of the United States. This virus will readily infect a huge range of orchard weeds, and dagger nematodes can quickly spread it between cherry and apple trees. However, nematodes move very slowly, so it can take time for the disease to spread and take hold.

You’ll be able to tell that your plants have this disease when the fruit starts to flatten on both sides. You may or may not see the leaves rolling up from the midrib on your trees. Unfortunately, there is no cure or control for this apple tree disease. As soon as you find a tree with this infection, you want to remove it before it spreads.

Freedom Apple by ☼☼Jo Zimny Photos☼☼ / CC BY-NC-ND 2.0

11. Flyspeck and Sooty Blotch

Even though these are two different apple tree diseases, it’s common to see them occurring together on the same tree when the fruit is almost mature. All apple varieties are prone to having issues with these diseases, the yellow varieties will get the most severe symptoms. This is a fungal pathogen that won’t damage your fruit severely. It’s still edible with this disease, but it’s much less valuable in the marketplace because it’s a challenge to sell, so commercial growers can have a huge problem with it.

Sooty blotch has several fungal species that can cause it, and it will produce symptoms that you would expect by hearing the name. The blotches can be a quarter of an inch in diameter or bigger, and they can cover almost the entire apple. You can rub the blotches off a lot of the time, but commercial growers would have to bleach the fruit early in the season to get rid of it.

The Zygophiala jamaicensis fungi causes Flyspeck, and the symptoms are what you’d imagine from the name. You could see 50 or more shiny black spots on the fruit’s surface. These are more difficult to simply rub to remove. Both diseases readily occur in damp and shady areas in the orchard. Opening up the trees and allowing more sunlight and air movement can ward them off. For the backyard gardener, you won’t have to worry too much about these apple tree diseases. The fruit will be fine to eat if you wash, rub, or peel it first.

Johnny Apple by katie hargrave / CC BY 2.0

12. Frogeye Leaf Spot and Black Rot

The same fungus will cause both of these apple tree diseases, but they occur at different points during the tree’s life cycle. The first sign that you have an infection is seeing brown spots on the ends of the fruit. These small spots will slowly grow to form concentric circles that will rot the apple. The leaves on the tree can also develop small holes or brownish-purple spots that look like a frog’s eye. This is when the disease is frogeye leaf spot. When the disease spreads to the tree’s limbs and causes cankers to form, it’s black rot.

You want to prune all of the infected parts of the tree as soon as you notice it and burn or get rid of them as fast as you can. You can spray the trees with a fungicide or sulfur in the disease’s early stages. However, by the time you can see infection signs, it could be far too late for fungicides to help you.

Black Rot by Scot Nelson / CC0 1.0

13. Powdery Mildew

There are dozens of powdery mildew pathogens, and they are all specific to different plants. Podosphaera leucotricha is the apple tree disease’s pathogen. The white growth on the undersides of the leaves that looks a lot like felt is a classic symptom. As the disease progresses, it can stunt your apple tree’s growth. The foliage will start to wilt as well, and the twigs and leaves will get more covered in specks that look like tiny black pinpoints.

If you plant your apple trees in a location with full sun and plenty of space between them, they are much more resistant to this apple tree disease. If you spot symptoms on your trees, you want to prune away any shoots that are white during the early spring months and destroy them. You should disinfect the pruning shears after you finish. If this is a common issue in your area, you can spray the orchard with fungicide or sulfur in the early spring months.

Cucurbit powdery mildew by Scot Nelson / CC0 1.0

14. Root Rot, Phytophthora Crown Rot, and Collar Rot

This trio of apple tree diseases are some of the most serious to watch out for. Various Phytophthora species cause them, and they’re very closely related to the pathogen that caused the Irish potato famine. They were once thought to be fungi, but they’re actually water molds or oomycetes.

It can be challenging to tell the symptoms from an infection by these water molds and other issues. The apple tree can be less vigorous, and the leaves may slowly fade to a yellow color. This disease group also attacks different parts of your tree. The crown is the area where the roots meet the stem on your tree, and the disease is called crown rot if this gets infected. Collar rot attacks the apple tree’s scion portions. In the more severe cases, the plant’s roots will rot. Infected trees will die, and this can be a very slow process or it can go as quickly as a year, especially if it’s very wet.

Once the soil gets infected, it’ll stay infected. You won’t be able to replant your apple trees in an area with these pathogens present. However, if you catch the apple tree diseases in the early stages, you have a good chance of saving the tree. You can spray the root area of the tree with metalaxyl or mefenoxam. Practicing good water management and planning ahead when you plant your apple trees can help you prevent these diseases. The soil should drain well, and you don’t want to overwater.

Hibiscus Root Rot by Scot Nelson / CC0 1.0

15. Rust

If your apple trees develop yellow or orange spots on the leaves, or if you notice that your apples are distorted or mottled, you most likely have a rust problem. This apple tree disease has several forms, and the most common in cedar apple rust. The rust disease category has a complicated fungus as the cause, and they actually live on another plant and spread to your apple trees using the host plant to attack.

The host is usually a type of juniper, or the eastern red cedar. Getting rid of these plants on your property can help prevent the disease from taking hold. However, the spores can easily travel for miles, so this may not be totally feasible for you. You can spray once a week with a fungicide or sulfur to prevent it if you know that this is an active apple tree disease in your location.

Rust, Geranium by Scot Nelson / CC0 1.0

16. Soggy Breakdown

A lot of people tend to put their fruit in cool storage to help boost the shelf life of the whole harvest. However, if your storage temperatures are too cold, this can result in fruit injury and chilling. Soggy breakdown is one issue, and it’s very common with the Honeycrisp cultivar. If you have it, the apple flesh will develop brown rings. You want to keep your fruit above 36°F to help minimize this apple tree disease from appearing.

1st September 2011 by George Armstrong / CC BY-NC-ND 2.0

17. Southern Blight

The Sclerotium rolfsii fungus can infect hundreds of plant species, and apple trees are included in the list. This is a very common apple tree disease in the southeastern part of the United States, and it forms a weblike mycelium that is white and grows on the lower parts or bases of your tree trunks when they get infected.

This disease will kill your trees very quickly, and it’s nearly always fatal. The good news is that your apple trees will get resistant to this apple tree disease as they mature and age. Those that get most severely impacted by these diseases are one to three years old. The best thing you can do is take preventative steps when the trees are young. Don’t plant your trees in spots where this is a known problem, and purge your organic materials from around the tree’s base. This is typically a food source for the pathogen.

Syngonium: Bacterial leaf blight by Scot Nelson / CC0 1.0

18. Sunscald

Fruit can sunburn, just like people can. The first warning sign that your fruit is having issues with sunscald is that the skin will develop flushed or yellow areas. These areas will eventually turn dark before the fruit is fully ripe and still on the tree. You want to avoid these fruits when you harvest your apples because it won’t store very well. Since an infectious organism doesn’t cause this apple tree disease, you can put any impacted fruit in the compost pile.

Along with big areas of your fruit changing to yellow, it can start out as smaller yellow splotches that are very easy to miss. The spots get much worse if you harvest the apples and store them. Proper training or pruning can help manage this problem. Some farmers or gardners employ overhead irrigation to cool the fruit, but this can open the door for more apple tree disease problems, so you want to avoid this process.

Orchid: Sunscald on Leaf by Scot Nelson / CC0 1.0

19. White Rot or Bot Rot

White rot is called bot rot, and it gets its name because the Botryosphaeria dothidea pathogen causes it. The causal agent that causes this disease is actually very weak, and the infection will only start to be an issue if your apple trees are stressed out. However, if you do have a problem with this apple tree disease, you can lose the majority of your fruit. Cankers will form on the tree in the early summer months to make the new infections highly visible.

You may have problems telling this apple tree disease apart from black rot cankers, so you might end up sending samples into your local agricultural agency to narrow down which fungus is the root cause for your problems. You can have two types of fruit rot with this infection. The first one affects the external surface of the apple, and it’ll cause brown spots that are slightly sunken and have a red halo around them. If it progresses, it can rot the entire apple. The second type causes white rot, and the fruit will actually bleach as they turn a light brown and decay.

Since this only happens if your trees get stressed out, managing them includes minimizing anything that could stress the orchard. This can include water stress, winter injury, insect damage, or other disease types. You want to prune away any dead wood on the tree to stop fungus from growing. Remove any mummified fruit you see because spores like to gather here before spreading.

Rotting Tree by Russell Wall / CC BY-NC 2.0

How to Prevent Apple Tree Diseases – Two Ways

A lot of apple tree diseases spread very slowly over several years, and they usually aren’t highly noticeable until they overwhelm the tree. Taking steps to prevent the diseases ahead of time can help to keep your orchards free of pests and healthy.

Between Cuts, Sterilize the Pruning Shears

When you prune the apple trees, you want to sterilize the shears between each cut you make. If you don’t, the risk of spreading diseases throughout the tree or from tree to tree is very high. You can sterilize them by dipping them in liquid solutions that contain 10 to 50% bleach or 70 to 95% alcohol. If you’re cutting back damaged limbs with fire blight, this is extremely important as it’s very contagious.

During Planting, Practice Good Water Management

You want to ensure that you have adequate drainage for your orchard. Don’t plant it in areas that flood a lot, in heavy soil, or in low spots. Make sure your graft union is high above the soil line. It’s critical that you stop the water from building up around the crowns of the trees or they can contract the Phytophthora disease that we outlined earlier.

Bottom Line

There are many apple tree diseases around that can wreak havoc on your orchard if you allow them to take hold and thrive. We’ve outlined several, and you can use this guide to keep an eye out, catch them early, and save your trees or take steps to prevent them altogether.