Tree Diseases: A Closer Look at Shot Hole Fungus

If your trees look like they’ve been standing in as scenery for a Western film, you might be dealing with shot hole fungus. The damage can look dramatic once it sets in, but it often starts quietly with just a few small spots on the leaves until the canopy suddenly looks peppered with tiny holes. Unlike some of the other diseases we've discussed, shot hole fungus, if left untreated, can be deadly to peach, apricot, and plum trees.

The good news is there are practical ways to manage it and reduce the risk of it returning. Learning what to look for (and what to do next) is the first step toward protecting long-term tree health.

Quick Links:

• What Is Shot Hole Fungus?
• Shot Hole Fungus Symptoms: How to Recognize It
• What Causes Shot Hole Fungus?
• Treating Shot Hole Fungus in Trees
• How to Mitigate Shot Hole Fungus
• Why Shot Hole Fungus Matters in Urban and Community Forests

What Is Shot Hole Fungus?

Shot hole fungus is a common tree disease that primarily affects stone fruit and ornamental trees, especially those in the Prunus family (such as cherry, plum, peach, apricot, and some flowering cherries).

Shot hole fungus spreads through fungal spores that move between trees and plant surfaces, and it can persist from year to year in infected plant material. In managed landscapes, nurseries, and urban plantings, it’s often considered a recurring issue, especially when conditions allow the disease to establish early.

While untreated shot hole fungus is can be fatal to peach, plum, and apricot trees, when it affects other trees or is recurring it can have a lasting impact. It will reduce overall tree health over time by weakening foliage, stressing growth, and increasing susceptibility to other problems.

Shot Hole Fungus Symptoms: How to Recognize It

Like some of the other tree diseases we’ve discussed, shot hole fungus is easy to recognize once you’ve seen it; its symptoms are very distinctive. It usually starts as small spots on the leaves, then progresses into the classic “shot hole” appearance. The tree literally looks like it’s been hit by buckshot as the damaged tissue dries up and drops out.

Symptoms can appear in spring or early summer, depending on the tree species and local conditions, and they’re most noticeable on new growth. It is, however, a progressive disease, with the symptoms noted below following a natural progression depending on the severity of the infection.

Common Shot Hole Fungus Symptoms

• Small circular leaf spots
  Spots often begin as tiny purple, reddish, or brown dots scattered across the leaf surface.
  
  
• Spots that develop tan or gray centers
  As the disease progresses, the center of the spot may lighten, dry out, and become papery.
  
  
• “Holes” in the leaves
  The dead tissue in the center of the spot falls out, leaving clean, round holes that often make the leaf or leaves look like they’ve been hit with tiny pellets.
  
  
• Yellowing around leaf damage
  Leaves may develop a yellow halo around spots or yellow more broadly if infection is severe.
  
  
• Premature leaf drop
  In more severe cases, trees may shed infected leaves early, resulting in canopy thinning.
  
  
• Twig or bud damage (less common, but important)
  Some infections also affect twigs, causing small lesions or dieback, especially on young or stressed trees.

Shot hole fungus can look dramatic, but early recognition is useful because it allows for better timing of mitigation, cleanup, and prevention, especially in managed landscapes where trees are planted close together, and disease pressure can build quickly.

What Causes Shot Hole Fungus?

As noted above, shot hole fungus is caused by fungal pathogens that infect trees through leaf tissue and young twigs, most often when new growth is tender and more vulnerable.

A key part of what makes shot hole fungus so persistent is that it can, and does, survive between seasons in infected leaves, twigs, buds, and plant debris. When conditions are right, spores spread from that material onto healthy foliage, allowing the disease cycle to restart.

In managed landscapes, nurseries, and urban plantings, shot hole fungus is more likely to take hold when trees are under stress or when the canopy stays dense and slow to dry. This makes dormant season pruning and regular tree maintenance essential.

Over time, repeated infections can weaken overall tree health, making trees more susceptible to other pests and diseases.

Understanding the causes of shot hole fungus is an important step toward preventing tree diseases, especially for property managers and city teams responsible for maintaining healthy, resilient trees.

Treating Shot Hole Fungus in Trees

Like other fungal tree diseases, there really is no “cure” for shot hole fungus. Treating it is mostly about reducing disease pressure and preventing repeat infections, not trying to “cure” damaged leaves once symptoms appear.

Unfortunately, by the time leaves have holes, the infection has already happened, so the goal really becomes limiting the spread, protecting new growth, and supporting overall tree health.

For property managers, landscapers, and city forestry teams, a consistent treatment approach can keep shot hole fungus from becoming a recurring seasonal problem.

Start With Sanitation

This is the most practical step property managers and city forestry teams can take.

• Remove fallen leaves and potentially infected debris beneath trees whenever possible
  
  
• In high-visibility or high-risk sites, consider seasonal cleanup during and after leaf drop
  
  
• Don’t leave infected leaves in planting beds where spores can persist

Improve Airflow and Reduce Leaf Wetness

Shot hole fungus thrives when foliage stays wet.

• Dormant season pruning can help maintain an open canopy structure
  
  
• Avoid dense, overcrowded plantings when selecting and placing trees
  
  
• If irrigation is needed, prioritize drip irrigation over overhead watering

Support Tree Health to Reduce Severity

Healthy trees handle leaf disease far better than stressed trees.

• Water consistently during hot weather, and consider winter watering in dry regions
  
  
• Avoid over-fertilizing (especially high nitrogen)
  
  
• Reduce compaction and improve soil conditions where possible
  

Fungicides 

In recurring problem areas or high-value trees, fungicides may be used as part of a preventative plan.

• Fungicides are most effective when applied early, before widespread leaf damage occurs
  
  
• Timing and product selection matter, and treatment should follow label directions and local guidance
  
  
• For many municipal and commercial landscapes, fungicide programs are best reserved for trees where disease impact is repeated and significant
  
  
• Spray twice yearly, once after leaf drop and once in late winter before trees bud

Know When It’s “Manage, Not Fix”

Untreated shot hole fungus can be fatal, but spraying can help reduce its recurrence. When treated, it may not be fatal but it can:

• Thin canopies over time
  
  
• Increase stress during hot summers
  
  
• Reduce ornamental quality in public landscapes

Proactive and preventative care are often your best options. With consistent tree maintenance and good canopy management, most sites can significantly reduce the impact year after year.

How to Mitigate Shot Hole Fungus

Shot hole fungus is one of those tree diseases that can recur if conditions remain favorable year after year. Mitigation is less about a single “fix” and more about reducing the disease’s ability to cycle through a landscape and limiting the factors that can make the environment inviting.

For properties and urban sites with multiple susceptible trees, mitigation strategies include:

• Build airflow into the canopy long-term
  Maintain a pruning structure that prevents dense, shaded interiors where leaves stay wet.
  
  
• Reduce splash and prolonged moisture
  Adjust irrigation practices and site conditions so foliage isn’t staying damp for prolonged periods.
  
  
• Plan seasonal cleanup as a standard practice
  Treat leaf litter removal as part of your disease mitigation plan, not just aesthetics.
  
  
• Limit stress during peak heat
  Trees dealing with repeated leaf loss are more vulnerable to summer stress. Consistent watering and soil health support help reduce compounding decline.
  
  
• Monitor early and respond quickly
  The earlier symptoms are spotted, the easier it is to reduce the spread and protect nearby trees in the same planting zone. Include regular tree monitoring and tree inventories in your urban forest management.
  
  
• Choose resilient trees when replacing or expanding plantings
  In landscapes with recurring disease pressure, mitigation often starts with smarter tree selection, especially when trees are planted in groups. Working with a wholesale tree nursery can help you not only select the best native trees and cultivars for your needs, but they can also help with proper planting and placement.

In urban and managed landscapes, mitigation is about stacking small, consistent practices that reduce disease pressure over time. This will help keep trees healthier, canopies fuller, and maintenance needs lower. Long term, that translates to saved resources, both time and money.

Why Shot Hole Fungus Matters in Urban and Community Forests

In urban and community forests, trees are often planted close together, share irrigation zones, and face many of the same stressors. That proximity makes shot hole fungus more than just a cosmetic issue. Once it’s present, it can rapidly cycle through a landscape, moving from tree to tree via moisture, wind-driven rain, and infected debris.

Over time, repeated infections can lead to thinner canopies, increased summer stress, and declining tree performance, especially in parks, streetscapes, HOAs, and managed commercial properties where consistency and appearance matter.

If you’re seeing signs of shot hole fungus or want help preventing it, reach out to the SuperTrees team. We can support you with guidance on tree diseases, tree maintenance insights, and, as always high-quality nursery stock. Whether you need tree services, help selecting the right trees, or planting assistance, we’re ready to help.