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Written by: Lisa Edwards, DVM and Sharon Spier, DVM,Ph.D., DACVIM

Flies are a bane to barn life; they not only transmit disease but also irritate horses (and us). Before we dive into control methods, let's review fly species you might face. Fly MaskIdentifying them can help you create an effective fly control plan. 

The housefly, Musca domestica, and the face fly, Musca autumnalis, are non-biting flies that feed on eye secretions, nasal discharge, wounds, manure and on moisture around genitalia. The stable fly, Stomoxys calcitrans, is a biting fly that uses a piercing mouthpart to feed on blood and tends to target horses' lower limbs and abdomens. The horn fly, Haematoba irritans, is a biting fly that generally feeds on cattle but might bit horses housed nearby.

Houseflies and stable flies typically reproduce in manure, wet straw bedding, garbage and poorly composted manure. Face flies and horn flies only breed in fresh cattle manure. Adult face flies do not like to feed in dark barns or shady areas.

The housefly is commonly found in hot summer months; the face fly and stable fly are usually seen from mid-spring to summer and sometimes into early fall. Houseflies and stable flies breed year-round in tropical and subtropical regions, but they hibernate in temperate regions during cooler weather. Tabanids, such as horseflies and deerflies, generally prefer sunshine and avoid shaded places; they are inactive at night.

Culicoides species are biting gnats that breed near water. Their preferred biting sites vary; some feed near the mane and tail, while others prefer the abdomen, legs or face. They are weak fliers, don't travel far and are most active at sunset.

Disease Vectors

Here are some of the conditions flies cause and diseases they transmit:

Summer sores

Houseflies, face flies and stable flies transfer parasitic nematode larvae (e.g., Habronema species) to moist areas around the eyes, nostrils, mouth, genitalia and wounds. The larvae can't complete their life cycle in these tissues and incite a hypersensitivity reaction, resulting in chronic non-healing wounds.


Face flies transmit Thelazia lacrymalis, a nematode worm that resides in eye glands and ducts, resulting in irritation and secondary infection.

Pigeon fever

Houseflies, stable flies and horn flies can spread the bacterium Corynebacterium pseudotuberculosis, the causative agent of pigeon fever. Infection most commonly leads to external abscesses, though some horses develop more serious forms including internal abscesses and ulcerative lymphangitis (infection of the limb).

Equine infectious anemia virus

Horseflies and deerflies use their large piercing mouth parts to transmit the often-fatal virus from one horse to another.


Biting flies and gnats can induce hives, intense itching, hair loss, skin thickening, excoriations (abrasions) and skin ulceration that can predispose to secondary skin infection.


Culicoides species are the intermediate host for the nematode parasite Onchocerca cervicalis. The immature forms (microfilariae) of this worm are found in horses' skin (often at the midline of the abdomen); adults reside in the nuchal ligament of the neck. The microfilariae cause skin irritation that results in scales, crusts, ulceration, hair loss and skin pigmentation loss.

Fly Control Methods

Proper sanitation and manure management are the most effective fly control methods. Simply remove breeding ground, and they won't proliferate. Here are some ways to do this:

  • Quickly remove manure, excess feed, wet straw/hay and other organic debris.
  • Close garbage containers tightly, and clean them regularly.
  • Locate manure sites as far from stables as possible, or move them off property. Flies can travel miles to find your horse.
  • Move round bales regularly, and clean the feeding area.
  • Modify paddocks, stalls and watering systems to avoid water accumulation.
  • Cover composted manure with a fly barrier such as plastic.
  • Spread manure thinly on non-grazing pastures to facilitate rapid drying.
  • Mow, because flies often rest in shady areas of vegetation.
  • Place fly spray systems, fly traps (insecticide baits, pheromone lure or sugar lure) or resin "ribbons" in the barn, and apply insecticides (pyrethrin, permethrin) to surfaces where flies rest.
  • Release fly predators. These wasps lay their eggs in fly pupae, then kill the developing fly larvae. Removing manure and using insecticide, however, will also adversely affect these beneficial insects.
  • Feed insect growth regulators to horses daily or every other day. Treat all horses on the property for maximum efficacy.
  • Use horse protection, such as fly masks, sheets and boots; strong fans; and fly repellent sprays and spot-on treatments.

Contact your local extension agent for advice on controlling the fly species you're struggling with around your barn.


Article provided courtesy of AAEP Media Partner, The Horse.