Ask OGS: Rust on Apple Trees


It looks like we have some sort of orange fungus growing on our apple trees. What is the best way to fight this while keeping our apple trees organic?

Thank you,


Dear Beth,

Fungal gall on cedar tree, which causes rust.

Gelatinous gall on cedar tree - photo by Aaron Apple

The orange spots on your apple trees are a type of rust. Apples are susceptible to three kinds of rust: cedar apple rust, quince rust, and hawthorn rust. All three rusts are caused by spores that overwinter as galls on trees in the juniper family—especially the Eastern red cedar, Juniperus virginiana. Spring rains cause the galls to swell and produce gelatinous “horns” that start producing spores. Only one large gall can produce billions of spores. The spores are quickly released during wet periods in spring and are carried on air currents infecting apples, crabapples, quince, pear, Hawthorn, serviceberry, and mountain ash. Cedar apple rust galls resemble something from outer space, and their spores can travel over 2 miles. Hawthorne rust spores have been known to travel almost 14 miles. What? Yes...14 miles. In late summer, the apple (or host tree) produces spores that can, in turn, infect the cedar tree. Here is a chart about all three rusts.

The primary infection period on apple trees is between the pink stage and three weeks after bloom. Once the spores have been released for that year, there is no secondary infection period. Most of us won’t even notice that our trees have rust initially, but by early summer, the orange spots on leaves and fruit are easily visible. Once the trees have been infected, there is not much you can do for that year.   

Options to Control Rust for Organic Gardeners

  • Removal of Cedar Trees

    Eliminating all red cedar trees within at least a 500’ radius (preferably a 2-mile radius) of apples and other susceptible trees would be the ideal remedy for this problem, but that is impossible in urban settings.

  • Planting Resistant Varieties

    From an organic maintenance perspective, choosing rust-resistant apple varieties is imperative, and more than one cooperative extension site emphasized the importance of selecting resistant cultivars.  Farmer Tom Elmore grows only disease-resistant apple varieties, and he reports seeing very little rust on his trees. However, I have seen a lot of rust showing up on cultivars that are less disease resistant. Choosing resistant cultivars is tricky because a particular cultivar may be very resistant to cedar apple rust but highly susceptible to quince rust. Cultivars must be cross-referenced for resistance to each one of the rusts. The most important rust to watch out for in WNC would be cedar apple rust. Additionally, I highly recommend cross-referencing apple cultivars for susceptibility to the dreaded fire blight (very prevalent in the southern Appalachians). Here is a chart that cross-references the main apple diseases. I suggest cross-checking lists on various sites, checking for updated lists, and finally compiling your own list - especially if you are researching fireblight-resistant varieties because sometimes the information is conflicting.

Rust Prevention With Fungicides & Fungicide Possibilities

If you have a susceptible tree that you want to protect from rust, organic solutions can be tough. The keywords here are prevention and timing. Proper timing of the fungicide applications is vital to prevent rust. Fungicides should be applied from the pink stage until about three weeks after bloom. For Certified Organic growers, many of the allowed fungicides were allowable only with restrictions, so growers should check with their certifier before application of fungicides. According to the labels, Seranade, Copper, Oxidate, 70% Neem, and Sulfur will control rust, but it is somewhat mind-bending to navigate the particulars of the next paragraph. 

  • Bordeaux mixtures are a combination of copper sulfate and lime (calcium hydroxide), and they work to control both fungus and bacteria (like fire blight). Baby leaves are very sensitive to copper, so Bordeaux mixes are usually applied when the plant is dormant.

  • Copper should not be applied from 1/2” green through 4-5 weeks past bloom as it can cause damage to fruit (russeting) and leaves and should always be used cautiously once foliage appears. Many coppers are not labeled for use on apples past petal fall.

  • Lime Sulfur is also known as a concern in regard to fruit/leaf damage after tight cluster occurs (lime sulfur is really a dormant spray that should not be applied to plant foliage).

  • Oxidate can also cause russeting and must be applied at exactly the right time to be effective.

  • Sulfur washes off easily, so you may need to reapply it every 3-5 days, and you will need to apply it just before it rains (do not use sulfur if you have applied an oil spray within the last month or when temperatures are expected to exceed 80°).

  • Neem applications should begin at the first sign of spring budding. Neem oil should be applied late in the day to prevent leaf burn and to protect bees

    Unfortunately, Neem and Serenade were not fully discussed on Cooperative Extension sites. In all cases, the leaves should be coated with the fungicide to the point of run-off.

Orchardist Michael Phillips mentions using elemental sulfur sprays in an older article and micronized sulfur in another. He says, “I use the minimum amount of sulfur I can get away with during this time—about three applications on average” and warns that “sulfur applied in excess…eliminates the microbial allies that are essential for keeping disease under control in a holistic orchard.” In his most recent book, The Holistic Orchard, he uses four holistic springtime sprays at (1) week of ¼” green, (2) early pink, (3) petal fall, and (4) first cover (7-10 days following petal fall). His holistic spray is a mix of 100% neem with a little soap, liquid hydrolyzed fish, effective microorganisms (EM’s), blackstrap molasses, and liquid kelp. Remember to always read and follow the safety precautions and instructions on pesticide labels. Whew! What else can you do?

  • Buoy the Trees Immune System

    Trees with cedar apple rust may lose some of their leaves, and fruit quality can be compromised. Over time, defoliation can weaken the trees, so you will want to prevent further stress on the tree during the growing season. Make sure you provide adequate water during dry periods. Respond quickly to other potential issues like fire blight. Applications of seaweed and compost tea can have a tonic effect. After leaf fall in autumn, remove infected leaves and fruit from the property.

  • Provide Just Enough Nitrogen

    New succulent green growth is always more susceptible to diseases and insects. Provide adequate amounts of nitrogen for growth, but not so much that you have an abundance of succulent growth. This is particularly true with fruit trees because your objective is to harvest fruit, not leaves. As an organic gardener, pay attention to the details of nature and use this knowledge to your advantage.

Beth, I hope this answer helps with next year’s apple crop. Bottom line: if you don’t want to spray at all, only buy cultivars that are known to be resistant to the main pest pressures in your locality. And always give your plants what they need to be strong and resilient. 

All the best,



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