Flies are an unavoidable part of horse ownership, but they don’t have to take over your barn or constantly irritate your horse. With the right fly control strategies for horses, you can significantly reduce fly populations and create a more comfortable environment.

Understanding how to manage these persistent pests is key to effective equine fly prevention. The more informed you are, the easier it becomes to protect your horse from the stress and health risks flies can cause.

What Kinds of Flies Bother Horses?

Horse fly – This large biting fly—goes by several names including bottleflies and gadflies. Adult female horse flies feed on blood, and can transmit diseases like equine infectious anemia (EIA), and tularemia.

Deer fly – Similar to horse flies, deer flies are large, biting flies that feed on a horse’s blood too, and can pass on EIA and tularemia. They are also known as green-headed flies, green flies or gadflies. Both horse flies and deer flies are considered “tabanids” because they’re in the tabinidae family of insects.

Black fly –Black flies are also known as “buffalo gnats” and “turkey gnats.” They are small, biting flies that can transmit a parasitic nematode worm. Their bites can cause scabby lesions on the insides of your horse’s ears and on the neck, chest and belly.

Stable fly – Stable flies are a biting fly that also feeds on your horse’s blood, targeting lower limbs and abdomens. They are most often seen from mid-spring to summer into early fall.

Horn fly – These biting flies mostly bother cattle but may bite a horse near a herd of cattle.

House fly – This species doesn’t bite at all but it does feed on eye secretions and nasal discharge. You’ll also see them abound on wounds, moisture around your horse’s genitalia and on manure piles. These are more common in the summer months.

Face fly – Similar to house flies, this fly feeds on eye secretions and nasal discharge. They’re also found on wounds, in the moisture around your horse’s genitalia and on manure piles. They abound from mid-spring to summer and into early fall.

Bot fly (Gasterophilus)– Adult flies lay their eggs on the horse’s body, typically on the legs. The horse experiences itching, which leads it to lick the eggs. Once licked, the larvae hatch in the mouth and are swallowed, eventually reaching the stomach, where they grow into large larvae known as bots, which are about the size of a honeybee.

Where Do These Flies Come From?

Horse and deer flies lay eggs near water and wooded areas but are strong flyers so they can travel many miles to reach animals. Stable flies and many other flies lay eggs in manure or in decaying organic material.

According to the Louisiana State University Ag Center, a female horse fly can lay anywhere between 100 and 1,000 eggs per year. The adult life span of a horse fly is 30 to 60 days and the females must consume a blood meal to produce fertile eggs. Male horse flies do not bite.

Can a Fly Hurt My Horse?

A bite from a horsefly or deerfly not only creates a wound but it can provide an entry point for a fly-transmitting disease such as equine infectious anemia (EIA).

House flies and face flies don’t bite, while stable flies do—but all three can transmit parasitic nematode larvae to sensitive areas like the eyes, nostrils, genitalia, and open wounds. The larvae cannot complete their life cycle in these areas. This can result in a chronic non-healing wound known as a summer sore orhabronemiasis.

Face flies can also transmit eye worms which can cause irritation and secondary infections caused by a Thelazia eye worm.

Pigeon fever can be transmitted by house flies, stable flies and horn flies. This infection can cause external abscesses, internal abscesses and ulcerative lymphangitis. Banixx Horse & Pet Wound Spray can treat this infection effectively.

How Can I Control Flies on My Property?

A multi-pronged fly control approach is best, especially if you’re dealing with more than one kind of fly.

• Start by properly managing manure. This will reduce breeding grounds for flies. Make it a habit to remove manure, old feed and hay, and any used shavings from your barn area.
• Close lids on garbage bins and empty them out frequently.
• Keep your manure pile as far away from your barn as possible, and have manure removed off site regularly.
• Drain standing water in low areas.
• Fly spray systems such as the Country Vet Automatic Flying Insect Kill System automatically sprays every 15 minutes and can be an excellent method of reducing fly populations in buildings.
• Using a premise spray like Elector PSP Premise Spray or Permethrin 10% is a powerful way to help control and reduce fly populations around your property. These sprays are adulticides that target adult flies at the source, offering long-lasting protection for barns, stable sand other outdoor areas.
• Biological fly control such as fly predators and fly eliminators are insects that reduce fly populations by preventing fly eggs from hatching which disrupts their growth cycle.
• Horse and deer flies tend to avoid shade so canopy trees or run-in sheds can offer some relief for your horses. These flies tend to bite in the daytime so nighttime turnout can also help.
• You can set traps for horse and deer flies in areas where flies congregate, but not where horses can access them. These traps attract flies with visual cues. For these species, place the traps in sunny areas away from buildings so the flies can see them.
• For stable flies, you can use traps such as scatter baits, sticky traps and jug traps however each one comes with some caveat. You must keep pets away from scatter baits. Sticky traps can easily snag your horse’s tail and too often you end up sacrificing the tail to a pair of scissors to remove the sticky bait trap. Jug traps stink horribly.
• Now for a permanent, environmentally friendly option albeit it a bigger investment upfront. Ceiling fans. Or, if your barn will not accommodate this equipment, a good supply of strategically placed box-fans does a great job. Fans tend to deter flies because it keeps the air moving making flight tougher for the fly.

How to Treat Fly Bites in Horses

Fly bites can cause discomfort, itching, swelling, and skin irritation—and some horses, particularly those with lighter coats or sensitive skin, may develop Insect Bite Hypersensitivity (IBH), a more severe allergic reaction to insect saliva.

Best Treatments for Fly Bites on Horses

1. Gently Clean the Affected Area

Start by cleaning fly bite wounds with a mild, horse-safe cleanser to remove dirt, sweat, and allergens. This helps prevent secondary infections and prepares the skin for topical treatment.

2. Apply a Topical Anti-Itch or Skin-Soothing Product

For horses that are prone to allergic reactions or have sensitive skin, using a soothing treatment is essential.

• EquiShield® IBH Salve or Spray are products that are specifically formulated for horses with insect bite hypersensitivity. These products not only repel insects but also help manage inflammation, itching, and skin irritation caused by fly bites. This product is unique because most other fly sprays only repel insects—they don’t treat the allergic skin reaction.
• Banixx® Horse & Pet Wound Spray or Wound Cream is an effective solution for treating wounds caused by biting flies, with the spray being completely safe for use around the eyes. If your horse has a wound that attracts flies, apply Banixx Wound Care Cream to help deter pests while promoting healing. This cream contains peppermint oil, a known natural fly deterrent, along with soothing ingredients ideal for irritated or open skin.

3. Use an Effective Horse Fly Repellent

Protect your horse from future bites with a quality fly repellent for horses. Look for natural options that contain citronella, cedarwood, lemongrass, or peppermint, such as:

• EquiShield® FG (Fly Guard)
• Sore No-More® Classic Ricochet Horse Spray

These products provide effective protection without harsh chemicals, making them great for horses with sensitive skin or allergies.

4. Monitor Skin and Reapply as Needed

Reapply fly sprays and skin-soothing products regularly, especially during peak fly season. If swelling, itching, or hair loss continues, or if there are signs of infection, contact your veterinarian for additional guidance.

For horses prone to Sweet Itch, a targeted supplement such as Summer Eczema Oral Powder can help support the immune response and reduce hypersensitivity to insect bites. The Summer Eczema supplement contains natural herbs specifically formulated to soothe the skin’s reaction to a severe allergic reaction to Culicoides midge bites.

How Can I Keep Flies Off of My Horse?

You can cover your horse with fly sheets, fly boots and fly masks. These will provide physical barriers against multiple types of flies such as stable flies, horse and deer flies and horn flies. One study shows that zebra stripes on a fly sheet can decrease horse and deer fly attacks because of the way these species perceive color.

If you’re going to use a fly repellent, you’ll want to apply products with synthetic pyrethroids all over your horse’s body. Try spraying fly repellant such as UltraShield® EX Insecticide and Repellent, Pyranha® Wipe N Spray Oil Base Equine Fly Spray or Repel-Xpe Emulsifiable Fly Spray Concentrate on a brush or microfiber mitt and applying it to the horse’s body. This may not prevent biting flies from flying around your horse, but it can reduce bites. Always read the product label carefully to determine how often to apply the fly repellent for horses, as application frequency can vary by brand and formula.

Be careful of how you dispose of fly repellant or pest control products to avoid contaminating the ground water or poisoning children, pets or other animals.

How Do You Keep Horse Flies Away Naturally?

Looking for a natural fly repellent for horses? Products like EquiShield® FG (Fly Guard) and Sore No-More® Classic Ricochet Horse Spray offer effective equine fly protection using essential oils such as citronella, cedarwood, lemongrass or peppermint to naturally repel flies without harsh chemicals. These natural repellents are available in sprays, roll-ons, and salves, giving you flexible options to suit your horse’s needs and preferences.

Important Tip: While fly repellents may not always work against black flies, horse flies, and deer flies, products containing DEET, citronella, lemongrass, peppermint oil, or geraniol have been shown to be more effective—especially for repelling horse flies. For best results, choose a repellent formulated with these proven ingredients. These natural options provide gentle, effective solutions for fly control—especially during peak fly season.

Why Fly Control Is Important for Horses

Flies on horses are more than a seasonal annoyance—they can lead to discomfort, skin infections, and even transmit serious diseases. Implementing an effective fly control routine for horses is essential for maintaining your horse’s health and comfort. Whether you choose horse fly sprays, spot-on treatments, fly sheets, or traps, consistent use of the right products can make a big difference. Combine these tools with proper barn hygiene to create a strong defense against flies. By prioritizing equine fly prevention, you’ll help ensure your horse stays healthy, stress-free, and protected all fly season long.

If you have more questions about fly protection for horses call us at 800.786.4751.

Originally written by: Abigail Boatwright. Reviewed and updated by Dr. Frank Reilly.