Brown or black spots on apple tree leaves? A practical guide

Having my own apple tree, I had to do a lot of research myself last year when I encountered this problem. As I’m relentlessly interested in trees, as usual I went overboard and learned all about it in depth! There are a number of causes of spots on apple tree leaves, whether they’re brown, black, purplish or green… but what’s wrong with your tree or trees?

In general, brown or black spots on apple tree leaves are caused by one of four fungal diseases – apple scab, cedar-apple rust, alternaria blotch or frogeye leaf spot. These vary subtly in appearance and their prevalence is related to geographical location. They have different control methods.

However, it took me quite some time to find good resources (and helpful books, bought off eBay) to do this. I would love to provide you with a straightforward guide to actually diagnosing your apple tree problem, so that you’ll know how serious it is and have a good shot at fixing the issue. That’s what Hands-On Gardening is all about.

So I’m going to take you through the ‘big four’ leaf diseases one by one and a few other causes as well. There’s a handy comparison table as well if you scroll down. By the way, this article will be a help for you whether you’re growing an ornamental or crabapple tree, or have your own home orchard – these trees of the genus Malus are all closely related and all are afflicted by these spotting conditions.

If you’ve got brown or black edges or tips on your leaves, rather than spots throughout the leaves – scroll down to the bottom past the fungal diseases, where I’ll tell you the causes of that, and what to do to prevent it.

Apple scab – Venturia inaequalis

Apple scab leaf spots. Attribution: AfroBrazilianVenturia inaequalis 01CC BY-SA 3.0

This fungal disease tops the list as it’s the best-known of the diseases causing apple leaf spotting. Particularly as it can make the fruit inedible and is a huge issue for commercial apple growers.

Apple scab appearance

Green (usually described as olive green) leaf spots on the upper or both sides of the leaves, which turn brown over a period of weeks. The spots have indistinct edges and are variable in shape. Sometimes the spots can be along the leaf veins. As the disease progresses, the spots can sink into the leaf (making a cupping or pitting shape). The spots can have a velvety feel.

Which parts of the world is it seen in?

All over the world – but generally temperate areas. It survives low temperatures.

When does it appear

It’s usually seen spreading rapidly on new leaves in spring, particularly when the temperature warms up (above 55°F/12°C) in combination with wet weather.

Where does it spread from?

It overwinters in fallen leaves on the ground. Spores then spread to trees through wind and rain.

Does it affect tree growth?

It can do – the leaf spot decreases the area of green foliage, but more significantly it can cause extensive leaf drop. This reduces the tree’s ability to manufacture sugars and can stunt its growth.

Does it affect the fruit?

Definitely. It causes enlarging brown ‘scabs’ on the fruit which, when advanced, are ‘corky’ in consistency.

What do I need to do?

If you can’t completely replant with a more resistant variety, the most important thing is control, not cure. Once the infection’s taken hold it’s too late for that season, though you could do some controlled pruning of diseased areas. Make sure you sterilize your secateurs with rubbing alcohol or alcohol-based hand-sanitizer in between cuts though, and then bag up and burn what you cut off.

It’s the same for fallen leaves and fruit – it should all be carefully raked up and removed. If you go over it in the mower it’s more likely to decompose, which might be somewhat effective.

The aim is to prevent reinfection next spring. Commercial fungicide can be sprayed on as new growth appears in the spring. Be sure to follow the manufacturer’s instructions and not to overdo it, as you can end up harming the tree. If you want to eat the fruit, but want to use fertilizer, you should contact a trained arborist for advice first of all.

Here’s a particularly useful video about reducing the spread of apple scab spores, produced by Michigan State University.

Cedar-apple rust: Gymnosporangium juniperi-virginianae

This leaf spot fungus is different from the rest, in that it only spends some of its time in apple trees – it needs a tree of the juniper family to be relatively nearby, to act as its other ‘host’ – usually this is eastern redcedar (Juniperus virginiana).

Cedar-apple rust appearance

The spots are definitely ‘rust’ coloured – a tan, orangey brown and around a quarter of an inch in diameter. The border can be reddish. The spots grow these finger-like projections called telia, which stick out or dangle from them.

Which parts of the world is it seen in?

It’s common wherever eastern red cedar trees are common and growing natively – this is particularly in the eastern half of the United States.

There are a number of similar rust fungi affecting the apples in other countries, for example in the UK – but they would be far less common.

When does cedar-apple rust appear

Cedar-apple rust spots show up on new apple leaves in spring when the temperature rises above a certain threshold- according to the University of Missouri, that’s 52°F (11°C). Provided there is enough humidity or rainfall, it can spread quickly through foliage.

You may get a clue from nearby juniper though – see below.

Where does it spread from?

Look for large orange ‘galls’ (they’ve been likened to Christmas tree baubles) with string-like projections on nearby trees of the juniper species, especially eastern red cedar – these are sometimes called ‘cedar apples’ and release spores in the spring which land on young apple leaves.

These alternative hosts may be as much as a mile away though, since the spores are carried very effectively by wind.

Does it affect tree growth?

Not really – it isn’t a serious infection, and could be seen as more cosmetic.

Does it affect the fruit?

Usually not – only if it’s a variety that particularly sensitive to this pathogen.

What do I need to do?

If you have eastern red cedar on your property, the spiky galls can be cut off to stop them from releasing spores in spring (or the trees themselves can be removed… that’ll do it, as long as there aren’t any other ones half a mile down the road…).

Some think it’s fine to tolerate these brown spots, and since the infection doesn’t do much harm to the tree, some would even encourage you to try to learn to appreciate them!

However it is sensitive to fungicides, especially myclobutanil. All fungicides must be sprayed as per the manufacturer’s instruction. The aim of the treatment is to prevent the brown spots from forming, by spraying the tree during that period when new leaves are appearing. Once spots have formed, it’s too late for that summer and you’ll have the chance to try again next year.

Remember if you’re planning to eat the apples, I recommend a professional’s assistance before you spray anywhere – contact an arborist.

This video from plant pathologist Mary Ann Hansen’s gives a great overview of cedar-apple rust.

Alternaria blotch: Alternaria mali

Alternaria’s another significant infection that can cause severe blight in some cases. It has spread significantly over the past 20 years.

Alternaria appearance

This one is darker brown, or even rather black, when compared with apple scab or cedar-apple rust. The spots, often initially like tiny dots, have a well-defined, purplish border to them. They can enlarge in size up to a quarter-inch (6mm) in size and can coalesce (join together).

The affected leaves tend to be fairly evenly distributed throughout the canopy.

Which parts of the world is it seen in?

This fungus likes warmth and humidity – it has caused big problems in India’s orchards. It’s found across the southern United States but hasn’t yet made inroads into the north. It’s not known to be present in the UK, or widespread in Europe.

When does it appear

Late spring or early summer. According to Pennsylvania State University, optimal conditions for spread are achieved in wet weather when the temperature rises to 77°F (25°C).

Where does it spread from?

This survives through winter on old leaves on the orchard floor, as well as in damaged twigs on the tree, from whence spores reinfect new leaf growth.

Does it affect tree growth?

It definitely can, by means of significant leaf loss (these leaves often turn yellow before falling off). Once a significant number are lost, this greatly reduces the tree’s ability to synthesize sugar using sunlight and thus can be detrimental to its overall growth and vigor.

Does it affect the fruit?

Yes – it can appear small dark spots, which are sometimes raised, on the apples. It also can cause premature fruit drop.

What do I need to do?

Like many of these infections, certain cultivars are more, or less susceptible. ‘Jonathan’ is a particularly naturally resistant cultivar of Malus domestic. But if you don’t want to start over with new trees, there are some ways to control, if not totally eliminate, the infection.

What’ll make the biggest difference is careful collecting of all fallen leaves, fruit and twigs, so the infection has nowhere to overwinter and can’t spread spores to new growth the following year. If it’s a challenge to pick up everything, it may help to mow over whatever’s left in fall to encourage it to decompose.

Pruning off twigs with infected leaves isn’t part of the plan here – again you’re trying to interrupt the fungus’ life cycle by maintaining good hygiene practices.

Fungicides again can be effective and are usually used throughout spring and summer in accordance with the manufacturer’s recommendation. Again, if you want to eat the apples from your tree, don’t spray yourself but rather consult an arborist.

It’s also long been noted that trees are heavily infected by mites, which feed on the leaves by sucking. A mite treatment programme might help a severely threatened tree as well.

Frogeye leaf spot: Botryosphaeria obtusa

This fungus, used to be called ‘common leaf spot’. It’s also known as Sphaeropsis leaf spot. It looks really similar to alternaria blotch. Though when it affects the fruit itself, we call it black rot, which doesn’t sound great…

Black rot of apple that follows frogeye leaf spot. Clemson University, Botryosphaeria obtusaCC BY 3.0

Frogeye leaf spot appearance

It’s difficult to tell frogeye spots from alternaria blotch. The spots also tend to be dark brown or blackish with a well-defined purplish border, and also grow to a maximum of about a quarter-inch in diameter. There can be up to 50 spots per leaf.

One difference may be that alternaria is more evenly distributed throughout the leaves of a tree’s canopy that frogeye leaf spot it. Certainly, if you see fruit that are affected by large brown patches or which is shrivelling up, you know it’s Botryosphaeria obtusa.

The name refers to their tendency to develop a tan color centrally later on, which along with a brownish border make a ‘frog’s eye’ appearance.

Frogeye leaf spot can affect other plants – it’s particularly of interest to soybean farmers.

Which parts of the world is it seen in?

It’s often seen in the United States – particularly in the Midwest. Frogeye spot (and its corresponding fruit disease) has been found in temperate regions throughout the world, but there’s a lack of specific data about its prevalence worldwide.

When does it appear

The spots are seen on new leaves, beginning in early spring and throughout summer, then appearing on developing fruit. There’s a risk of infection when the temperature goes above 50°F (10°C), especially if there are heavy rains. It spreads best in summer weather of around 75°F (24°C).

Where does it spread from?

It lingers over winter in old infected dried-up fruit and leaves, then can get onto new leaves by wind, rain splash and via insects. This one however can also survive winter on the apple tree itself, in wounds caused by pruning, insects of other diseases (such as cankers from fire blight, which affects many fruit trees including apple).

Does it affect tree growth?

Yes – because it can causes yellowing leaves that fall off early, reducing the tree’s photosynthesizing ability, over the course of years the overall health of the tree and its growth can be significantly impaired.

Does it affect the fruit?

It sure does – ‘black rot’ causes dark brown spots over the apple, which spread as large patches until the entire apple can become shrivelled up and ‘mummified’.

What do I need to do?

The goal is to reduce risk of reinfection the following growing season, since it’s largely too late for this year when the infection’s already taken hold and the spots are apparent.

Careful hygiene measures are most important – removal of dead leaves and twigs and old infected fruit from the ground near your tree or trees. If you can’t collect everything, running over it with a mower may help reduce the risk of spores release, as it helps the tissue biodegrade. If you have any piles of logs on your property, these can be a potential reservoir for infection as well.

Given that spores can also be released from cankers or infected damaged bark on the tree itself, it’s important to prune these out. But you’ll need to use careful pruning practices to avoid making the infection worse. Fire blight cankers are a common hiding place for infection – these look like wet or darkish areas on the bark. Check out this article for advice on how to prune out fire blight safely and effectively.

Wider control measures include complete replanting of more resistant cultivars. Biggs and Miller published a study in Horticultural Science in 2004, and ranked several cultivars of Malus domestic according to the resistance they showed to Botryosphaeria obtuse. ‘Golden Delicious’, ‘Creston’, ‘Enterprise’, ‘Fuji’, ‘Goldrush’, ‘Gala Supreme’ and ‘Braeburn’ appeared to have the most natural resistance to the infection.

The application of fungicidal spray is an important part of suppression of the disease in commercial orchards. These are often applied just as the leaf buds are about to open. It’s important to apply any fungicide in accordance with the manufacturer’s instructions – there isn’t a ‘one size fits all’ approach. But if you’re planning to eat any of the fruit, you should consult a trained arborist before any fungicide is applied.

Table: common diseases causing spots on apple tree leaves

Disease causing spots on apple tree leavesApple scabCedar-apple rustAlternaria blotchFrogeye leaf spot
Scientific nameVenturia inaequalis  Gymnosporangium juniperi-virginianae  Alternaria mali  Botryosphaeria obtusa  
AppearanceOlive green leaf irregular spots turning brown, up to ¼” diameter, one or both sides, develop cupping shape. Spots can feel velvety.Orange brown leaf spots around ¼” diameter with finger or horn-like projections arising from them. Bright orange galls may be seen on nearby juniper speciesDark-brown or blackish round spots with purplish border or hue, growing up to up to ¼” diameter and sometimes joining togetherSimilar to Alternaria blotch – but may be less evenly distributed throughout the tree. Center of spots turn a light tan giving ‘frog’s eye’ appearance
Geographic locationWorldwide – especially temperate areasEastern USA, especially where eastern red cedar is commonSouthern United States. Warm humid countries particularly in southern AsiaUSA Midwest. Other temperate regions of the world.
When the spots appearWet weather when temperature > 55°F/12°C  Springtime where there’s sufficient rain and humidity and temperature rises above 52°F (11°C)  Late spring/early summer, particularly when temperatures rise over 77°F (25°C) in wet weather.  Early spring and throughout summer, then on developing fruit. Starts in wet weather above 50°F (10°C) spreading readily at around 75°F (24°C).  
Spreads from whereFallen leaves on the ground, where the infection overwintersGalls on Juniper species, especially eastern red cedar, which can be up to a mile away (spores spread by wind)Through infected leaves and twigs on ground from the previous seasonLeaves, twigs and ‘mummified’ infected fruit on the ground; in damaged bark or cankers from fire blight infection
Affects tree growthYes, via reduced vigor from leaf lossNoYes, via reduced vigor from leaf lossYes, via reduced vigor from leaf loss
Affects fruitYes – brown spots and corky scabsRarely – only if a very sensitive cultivarYes – small dark spots on apples and early fruit dropYes – causes major fruit loss by ‘black rot’
Control methodsSanitary pruning. Removal of all fallen leaves and fruit. Fungicidal sprays in spring.Prune off galls on nearby eastern red cedar (or remove the trees themselves). Fungicidal sprays in spring.Removal of all fallen leaves and fruit. Fungicidal sprays in spring and summer. Treatment for mite infestations.Removal of all fallen leaves and fruit. Fungicidal sprays in spring. Sanitary pruning methods to remove damaged wood and cankers.  

Some other causes of brown spots on apple leaves

Spots that are seen over the surface of the tree’s leaves are usually caused by fungal infection, but if they’re all touching the tips or edges of the leaf, it’s probably due to other environmental reasons.


With underwatering you can see drying out of the leaf tips and edges, which go yellow or brown and can shrivel. This is particularly common in young trees which have recently been planted, and so haven’t established an effective root system. Young apple and crabapple trees need watering about once weekly when the weather is dry. When watering, you’re trying to soak the tree to its deeper roots – a forty minute soak once a week will be better than a ten minute soak four times a week.

If you’re not sure whether the tree needs water, just dig your finger an inch or so into the soil near the base of the tree. If the soil seems dry or it doesn’t stick to your finger – go for it. Dry to water the whole root area, and not just near the base.


Waterlogging the soil commonly causes blackening of parts of the apple tree’s leaves – the tips, or along the central vein. In common with many fruit trees, apple trees don’t do well when planted in soil that’s constantly wet.

Frost damage

While many apple and crabapple trees are quite hardy, freezing temperatures that occur at the wrong time (particularly in late spring when fresh and fragile new leaves are opening) can result in brown dead areas on the leaf margins, particularly near the tips.

Wind damage

Similarly, browning edges can be a sign of the apple tree’s susceptibility to high winds, particularly when young and during dry weather, when the wind can dry out those parts of the leaves. You may noticed the there is more severely affected on the side facing the prevailing wind. This is likely to resolve when the tree is older with a more established root system, but for now, you may need to water the tree more frequently, to protect against the dessicating effects of the wind.

You can buy horticultural fabric, a piece of which can be used to shelter the young tree and minimize this issue.


I hope you found this article helpful. Remember – while fungicidal sprays are part of control of each of the tree infections described, if you’re planning to eat any of the fruit, consult a trained arborist. That said, there is much that you can do yourself to prevent reinfection the following year through excellent hygiene. But remember to properly dispose of whatever you rake up – by burning it, or putting in the trash. Get your rake ready!

Check out this article that looks at a similar problem in pear trees.

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