The Resurgence Of The Fly Army In Early Fall
Animal Care Team
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Where There’s A Resurgence Of Flies In Early Fall
Just when you thought fly season might be ready to give you a break, late summer and early fall can bring an unexpected surge in fly activity. You’re not imagining things. Fly populations can rebound with surprising strength this time of year. Understanding why this happens, and how to fine-tune your fly control routine, can help keep your horse more comfortable through the final stretch of pest season.

Why Flies Rebound Late in the Season
Flies thrive in warm, humid conditions that persist well into September in many regions. By this point in the season, fly populations have gone through multiple breeding cycles, and the latest generations tend to hatch faster thanks to the sustained heat. The result? A noticeable increase in numbers just as fall approaches.
At the same time, fly predators such as certain birds and parasitic insects begin to taper off with the change in daylight and temperature. This reduces natural checks on fly populations, allowing them to multiply unchecked in barns and paddocks.
Meanwhile, areas around the farm, especially where manure, old hay, or damp bedding accumulate, can become ideal breeding grounds. Even slight lapses in manure management or sanitation at this point in the season can fuel a last wave of flies.
How to Adapt Your Fly Control Strategy
To stay ahead of this late-season spike, it’s important to stay consistent and even double down on your fly control efforts. Here’s how:
1. Keep Up with Physical Barriers
Fly masks, sheets, and leg wraps continue to be effective into the fall. Just make sure gear is clean, properly fitted, and free from rips that could allow pests in or cause irritation.
2. Use Fans to Disrupt Fly Flight
Flies are weak fliers, especially in strong airflow. Keeping stall or aisle fans running can help reduce their ability to land and bite—plus, it helps reduce moisture buildup in enclosed spaces.
3. Maintain Perimeter Control
Fly traps, bait stations, and premise sprays around the barn and turnout areas can reduce the overall fly population. This is especially helpful in late summer when breeding grounds are more abundant.
4. Step Up Manure Management
It can be tempting to relax your cleaning schedule as the days get shorter, but now’s the time to stay vigilant. Remove manure and wet bedding daily from stalls, paddocks, and around feeding areas. Keep compost piles far from horse housing.
5. Refresh Your Fly Spray Routine
If you’ve been using the same fly spray all summer, consider rotating to a different formula to prevent resistance. Look for a product with long-lasting protection that holds up in sweat and humidity. Try rotating to UltraShield® Red or UltraShield® Gold, which use different ingredients that some other fly sprays which the flies may not have encountered all summer.

Finish the Season Strong
Fly season doesn’t end when school starts or leaves begin to change color. By maintaining (and slightly adapting) your fly control routine, you can reduce the risk of irritation, skin conditions, and stress for your horse as the seasons shift. With a few simple steps, you can stay ahead of the late-season surge and keep your barn as pest-free as possible until the first frost.
References
- U.S. Environmental Protection Agency: “Controlling Flies in and around Horse Barns” https://www.epa.gov/sites/default/files/2015-08/documents/ipm-horses.pdf
- University of Kentucky Entomology Department: “Managing Stable Flies on Horses and Horse Farms” https://entomology.ca.uky.edu/ef502