Fly Control for Horse Farms

How to create a fly-control plan to protect your horse from annoying insects throughout the summer.


Fly season can be a miserable time for horses and humans. Aside from being nuisances, flying insects can be vectors (agents) for serious diseases, such as West Nile virus (WNV) and Equine Infectious Anemia (EIA).

Here are the main pests that bother horses.

Housefly (Musca domestica):

This fly mills around your horse’s face to lap moisture from his eyes and mucus from his nose with its sponge-like mouthparts. It will also feed from wounds or sweet things, such as grain. The Housefly is the most common pest. Although it isn’t a biting fly, it can still spread diseases.

Stable fly (Stomoxys calcitrans):

This biting fly resembles the housefly but has a pin-like mouthpart. It sits on your horse’s lower legs and flanks where it bites into the skin to suck blood with its tube-like beak. The stable fly is a strong flier and can travel miles.


The mosquito’s bite is itchy and unpleasant, and the mosquito can carry WNV and Eastern Equine Encephalitis (EEE.)

Horsefly and Deerfly (insect family Tabanidae; order Diptera.)

These strong fliers are sight hunters. It’s environmentally unsound to eradicate their breeding ground, since they choose to lay their eggs in natural marshy areas. These flies settle on their prey and then use their saw tooth to slash the skin, lapping up the resulting blood. They are vectors for the EIA virus. They don’t like shade, so horses will often head for shelter when these biting flies attack. Most fly sprays aren’t effective against horseflies and deerflies.

Strategic Control

How can you control such a wide range of pests? Use a multi-pronged approach.

  • Begin fly control when pests are most vulnerable. This can be at the beginning of the season, when pupae are hatching and emerging from their winter’s nest in the spring; when they are breeding; or when they are in the early stages of life.
  • Use fly traps correctly. Don’t place traps inside your barn because they’ll only attract flies in. Place traps away from the barn to lure them away. Put sticky traps in the barn to catch any lingerers; the sticky traps won’t attract more flies like the scent-baited traps do. Scent traps won’t work for stable flies because they are attracted to heat and not scent. Instead, use a prism trap to catch stable flies. This trap is made of a clear plastic and it mimics heat when light shines through it. When the fly investigates, it gets stuck on the adhesive inside.
  • Catch horseflies and deerflies with a deerfly trap, such as the Horse Pal Fly Trap, which works by luring the flies with a black ball. The flies move into the lighted part of the trap and then can’t find their way out.
  • If neighboring farms don’t have a fly control program, place traps or bait stations along your property line.
  • Practice good manure management. Fly pupae need ongoing moisture and rotting organic matter to develop into adults, which happens in a matter of days. Manure can be composted to eliminate flies. The manure will generate heat inside the compost pile and it will be too hot for flies to reproduce. Otherwise, pick up manure in pastures regularly or spread it thinly to dry it out if you can keep horses off the pasture for 2-3 weeks. Look for forgotten manure, such as in horse trailers or the wash rack drain.
  • Make your property inhospitable to pests. Rake wet spots to expose pupae. Fix leaking troughs or hoses. Halt mosquito development by dropping EPA-approved tablets into water troughs, and dump out standing water that isn’t in use. Stable flies can produce in rotting vegetation, such as grass and hay (one rotting round bale can host a million stable flies in one season, according to a Texas A&M study), so cover compost piles and remove old straw or hay bales. Sweep up spilled feed and dispose of it in a covered trash can to prevent houseflies. Pests like to cool off in tall grass and weeds, so keep weeds in check around your barn and paddocks.
  • Use fly barriers. Keep your horses comfortable by using fly masks, fly sheets and mesh leg wraps. Remove them and check for rubbing or wear once a day.
  • Use fly repellent correctly. Apply enough so that your horse’s coat is damp, and make sure that you spray his entire body. Flies will find areas not covered and settle there. Use a sweat-resistant repellent when riding or a long-lasting spray or spot-on repellent for pastured horses.

Population Control

There are two efficient ways to reduce the population of stable flies and houseflies: feed-through products and parasitic wasps. Both stop flies at the larval stage, before they become adults.

Feed-through fly control is a supplement that you mix with grain. It has an insect growth regulator (IGR) that travels within the intestinal tract and is passed in the manure without being absorbed by the horse. The IGR in the manure prevents housefly and stable fly larvae from developing an exoskeleton. For the product to work effectively, all horses on the property have to be on it. Properly dispose of untreated horse manure from visiting horses.

Another option is to use parasitic wasps, tiny insects that are harmless to humans and horses, but prey on the types of flies that breed in manure and rotting vegetation. The female wasp drills a hole through the fly pupa, lays her egg, and then the dead pupa becomes a food source for the developing wasp.

Flies around a horse's eye

Release wasps when the weather is at least 45 degrees for three consecutive days, which is just before flies start breeding. Use the proper dosage for your situation (suppliers have usage calculators on their websites), apply them monthly, and place them where flies breed, such as in urine and manure spots, around water troughs, manure piles and where decomposing organic material exists. Parasitic wasps also have no resistance to insecticides, so you can’t use overhead sprays. You can use fly spray, but make sure to you spray your horse away from any areas treated with wasps.

Fly season doesn’t have to be endured; with a little forward-thinking, you can control flies and have a pleasant summer.

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  1. Great advice. Having a couple of chickens around the barn is also a great way to clean up spilled feed.
    I wonder about the IGR in the manure though. I use the manure as fertilizer. Will it affect my beneficial plant insects?


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