Flies are more than just a nuisance to horses and their owners. Without proper fly control, these insects can transmit diseases to your horse and cause skin irritations.

Effective fly control for horses starts before fly season begins with environmental management strategies to prevent flies from breeding on your farm. You can also protect your horses from flies by adding features to your barns that discourage insects from hanging around horses.

Fly spray is one of the most common methods for controlling flies. But horses often need added protection from wearable fly gear to stay comfortable during peak fly season.

Feed-through fly control is also available for horses, and some supplements may help support skin health in horses sensitive to bug bites.

This article will review everything horse owners need to know about effective fly control for horses. Keep reading to learn how flies impact horse health and the best strategies for protecting your horse from biting insects.

Fly Control for Horses

Certain flies can act as disease vectors, while others are annoying to horses due to their biting behaviour. [1]

Pest avoidance behaviours in domestic horses can significantly impact other areas of horse health. [2] For example, repetitive stomping at flies can loosen shoes and damage hooves.

Flies can also unsettle horses during turnout or riding. Horses trying to run away from insects can easily injure themselves or others.

Types of Flies

Understanding the type of flies responsible for irritating horses can help you identify pests on your property and develop an effective fly control plan.

Common types of flies that can cause problems for horses include: [1]

  • House Fly: This non-biting insect feeds on manure, wounds, eye secretions, and nasal discharge of horses.
  • Face Fly: Another non-biting insect similar to house flies.
  • Stable Fly: Stable flies are biting insects that feed on blood and usually target horses’ lower limbs and abdomen.
  • Horse Fly: Female horse flies are fast, large flies from the family Tabanidae that have a painful bite.
  • Horn Fly: These biting flies cluster together on the backs of cattle and horses, where they feed on blood 20-30 times per day.
  • Deer Fly: Deer flies are larger than house flies. They have yellow and black stripes and may be mistaken for bees. They are found in wooded and damp areas and are most likely to strike the head and neck of moving horses.
  • Gnats: Small biting insects that are most active at sunset. These include black flies that irritate the horse’s ears and members of the Colicoides family that feed near the mane, tail, abdomen, legs, or face.

Health Problems

Some flies are vectors for certain diseases, while others can cause inflammatory conditions or allergic reactions.

Health problems associated with flies include: [3]

  • Summer Sores: Parasitic nematode larvae transmitted by house flies, face flies, and stable flies cause chronic non-healing wounds around the moist areas of the nostrils, eyes, genitalia, mouth, or pre-existing injuries.
  • Eyeworms: Face flies transmit the nematode worm Thelazia lacrymalis to horses’ eye ducts and glands, causing infection and irritation.
  • Pigeon Fever: Horn flies, stable flies, and house flies spread the Corynebacterium pseudotuberculosis bacteria responsible for pigeon fever. This infection causes external abscesses and can progress to a severe form of ulcerative lymphangitis or cause systemic disease and internal abscesses.
  • Equine Infectious Anemia: Deer flies and horse flies can transmit the potentially fatal virus that causes equine infectious anemia between horses.
  • Hypersensitivity: Horses with insect hypersensitivities such as sweet itch might develop hives, hair loss, itching, skin thickening, abrasions, and skin ulcerations in response to bites from biting flies and gnats.
  • Onchocerciasis: Culicoides species transmit the immature forms of the Onchocerca cervicalis nematode parasite to the horse’s skin. The adult nematode resides inside the nuchal ligament of the neck.
  • Aural Plaques: Black flies can transmit the herpes virus that causes warts and aural plaques in horses.

Fly Season

Flies are most active during warmer temperatures from late spring to early fall. Flies cannot survive freezing temperatures, and most species spend the winter beneath the soil in their pupal stage of development. [4]

Horse owners usually notice an increased fly presence when the ground thaws and temperatures rise. Proactive fly control should begin in the early spring to control populations on your farm before they become unmanageable.

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Environmental Management to Prevent Flies

Good stable management is your first line of defence against flies. There are several strategies horse owners and barn managers can follow to avoid attracting flies and prevent them from reproducing.

Manure Management

House flies and stable flies reproduce in manure. Effective manure management reduces their breeding opportunities and keeps old waste as far away from your horse as possible. [5]

Pick your horse’s stall multiple times daily to avoid attracting flies into the barn. Paddocks should also be picked once per day. Remove manure to a manure pile on the opposite side of your property and keep compost piles covered with a heavy tarp to protect them from flies.

If you spread old manure, spread it thinly on a non-grazing paddock, so it dries quickly.

Minimize Moisture

Several fly species breed in wet areas. Minimize moisture and mud on your property and clean up standing water. Don’t leave out unused buckets or other objects that might become inadvertent water receptacles. [4]

Modify stalls, paddocks, and watering systems as much as possible to avoid puddles. Muddy areas of mixed manure, dirt, and water are prime fly breeding locations.

Feed and Hay

Flies use damp, soiled hay as another breeding area. Exposed grain can also attract flies, so store all feed in containers with air-tight lids. If you measure meals in advance, use bucket covers or a towel to cover the prepared rations.

You should thoroughly clean feeders after meals to remove uneaten grain and supplements. Sweeping up damp hay prevents it from molding and attracting flies to stalls and turn-out areas.

Keeping the barn clean and sweeping spilled grain will also limit flies in the barn. All trash should be kept in rodent-proof containers.

Biological Control

Biological methods of fly control can be an effective way to reduce fly populations. These methods use natural predators of flies, such as tiny parasitic wasps that feed on fly larvae. The wasps lay their eggs inside fly eggs, which kill the pupae before they mature. [6]

Biological control impacts the environment less than chemical repellents. However, you have to strictly follow the manufacturer’s suggested schedule for the best chance at success.

Curtains, Shade, and Fans

Research shows that installing large fans in your horses’ living areas can substantially reduce the number of biting insects. [7] Shady, breezy areas also provide refuge for horses from flies

Fly curtains can prevent insects from entire buildings without cutting off airflow. The material is similar to fly sheets and acts like a screen. Owners can hang these curtains at the entrance of run-in sheds or barn doors.

Fly Traps and Insect Repellents

Fly traps are an affordable way to reduce the number of flies in your stabling area. Bait traps attract flies and trap them for simple disposal. Do not use fly traps inside the barn, or you may draw the insects closer to your horses.

Chemical insect repellents are helpful around barn perimeters. Some barns also have fly spray misting systems that automatically spray the barn and horses with insect repellent multiple times per day.

Fly Spray for Horses

Fly spray is the most common form of fly control used by horse owners. However, studies on the effectiveness of topical fly protectants produce mixed results. [8]

The type of fly spray you use and how you use it impacts how it works. To get the best results from fly spray, follow these tips:

  1. Measure and mix concentrated products according to directions given by the manufacturer.
  2. Groom your horse before applying the fly spray. The product can fall off a dirty horse with excess mud and dust.
  3. Systematically apply fly spray to avoid leaving areas where flies can congregate.
  4. Use enough fly spray to produce a repellent effect. Most manufacturers recommend one to two ounces of solution.
  5. Store fly sprays away from direct sunlight to preserve chemical integrity.

Water-Based vs. Oil-Based

Fly sprays come in two varieties: oil-based and water-based.

Oil-based fly sprays use oily ingredients to slow evaporation so they last longer. However, these sprays can leave a sticky residue or dry out the skin. They can also amplify the sun’s rays like a tanning oil and cause burns.

Water-based fly sprays are gentler on your horse’s skin but don’t last as long.

Fly Spray Ingredients

Fly sprays use insecticidal and repellent ingredients. Insecticides kill flies, while repellents only discourage the flies from landing on the horse.

Common fly spray ingredients include: [8]

  • Pyrethrin: Pyrethrin is a natural insecticide derived from chrysanthemums. This ingredient breaks down in sunlight, so most pyrethrin formulas include synergists to extend effectiveness.
  • Pyrethroids: These are synthetic forms of pyrethrin that don’t break down as quickly. Common pyrethroids used in fly spray include permethrin, cypermethrin, and resmethrin.
  • Piperonyl butoxide: This ingredient is a common synergist. It inhibits enzymes in the insect’s bodies, which gives pyrethrins more time to work.
  • Picaridin: This synthetic insect repellent mimics piperidine, a chemical found in certain plant species that blocks the insect’s ability to sense the horse.

Natural Fly Spray

Natural fly sprays use oils such as citronella, tea tree, and cedar to repel insects. Studies show citronella spray reduces observable pest annoyance behaviour in horses. [8]

Some owners use natural fly sprays because their horses react to chemical insecticides. However, other horses may be more sensitive to the oils used in these formulas. Pay close attention to the ingredients in your fly spray if you have a horse with sensitive skin.

Culicoides midges are notoriously unaffected by conventional fly sprays. They are repelled by fragrant extracts like lemon grass, lavender and eucalyptus. Barrier creams are also effective. Noxzema or a mixture of Vaseline and fragrant extracts works well.

Topical Ointments

Topical ointments that contain insect repellent can help protect wounds from flies. These formulas usually last longer and provide better protection for small areas than fly sprays.

Fly Protection Gear for Horses

Wearable fly protection puts a physical barrier between pests and your horse. Fly sheets, masks, and boots usually offer better protection than fly spray alone.

These items are usually made from breathable mesh material to prevent your horse from overheating in the summer. The best material for fly gear also provides UV protection, which can help prevent coat fading and sunburn.

Fly Sheet

Fly sheets are breathable blankets designed to prevent flies from biting your horse. They can be worn in warm weather and often feature light UV-protective material. Coverage options with a belly wrap and attached neck provide the most protection.

Like all blankets, you should regularly remove your horse’s fly sheet to keep it clean, and prevent rubbing.

Fly Mask

Fly masks keep flies away from sensitive structures on your horse’s face and have different designs to protect the eyes, ears, and nose. Horses can easily see through the mesh material.

This fly gear prevents your horse’s eyes from getting watery and swollen from repeated irritation by flies. Masks with attached noses can also protect white noses from sunburn.

Fly Boots

Fly boots cover the lower leg with mesh material from the top of the hoof to the bottom of the knee. These boots can help if flies cause your horse to stomp his feet.

Studies show fly boots are more effective than fly spray alone at reducing stomping behaviour in horses irritated by flies. [8]

Feed-through Fly-Control

Feed-through fly control products contain pesticides that mix with your horse’s fecal material inside the bowel and prevent the development of fly eggs in the manure.

Manure from treated horses shows a significant reduction of house and stable fly maturation within two weeks. However, these products will not affect flies that don’t lay their eggs in manure. [9]

Feed-through products often use the active ingredients diflubenzuron and cyromazine. These ingredients were thoroughly safety tested as part of their registration requirements with the EPA and are widely considered safe for equine consumption. [9]


Some natural products use garlic to make the horse less attractive to flies. There is limited research to support the use of garlic for fly control in horses. Other commonly used natural ingredients such as B vitamins or brewer’s yeast also lack proof of effectiveness.

Furthermore, studies suggest there is a risk of Heinz body anemia in horses fed garlic for extended periods. [10]

Horses with insect bite hypersensitivity may benefit from an omega-3 supplement such as Mad Barn’s W-3 Oil. Studies show omega-3 fatty acids can significantly reduce the allergic response associated with sweet itch. [11]

w-3 Oil

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  • Promotes joint comfort
  • Helps to fight inflammation
  • Skin & coat condition
  • Palatable source of Omega-3's


  • Fly control is essential to horse health because biting insects can transmit infectious diseases.
  • Stable management can help reduce fly populations by removing manure quickly, minimizing standing water in paddocks, and keeping barn areas clean.
  • Insecticides, repellents, and physical barriers deter flies from horses and buildings.
  • Fly spray and fly gear help improve horse comfort during fly season.
  • Feed-through fly control is effective against flies that reproduce in manure, but not other species.

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  1. Burg, J. et al. Arthropod Faunal Composition on Kentucky Equine Premises. J Med Entomol. 1991.
  2. Keiper, R. et al. Refuge-seeking and pest avoidance by feral horses in desert and island environments. Appl Anim Ethol. 1982.
  3. Onmaz, A. et al. Vectors and vector-borne diseases of horses. Vet Res Comm. 2012.View Summary
  4. Rochon, K. et al. Stable Fly (Diptera: Muscidae)—Biology, Management, and Research Needs. J Integr Pest Manag. 2021.
  5. Lazarus, W. et al. Costs of Existing and Recommended Manure Management Practices for House Fly and Stahle Fly (Diptera: Muscidae) Control on Dairy Farms. J Econ Entom. 1989.
  6. Khoobdel, M. et al. Natural host preferences of parasitoid wasps (Hymenoptera: Pteromalidae) on synanthropic flies. Eur J Transl Myol. 2019.
  7. Lincoln, V. et al. Protection of horses against Culicoides biting midges in different housing systems in Switzerland. Vet Parasitol. 2015. View Summary
  8. Mottet, R. et al. Effectiveness of Stable Fly Protectants on Adult Horses. J Equine Vet Sci. 2018.
  9. Karasek, I. et al. A review on the treatment and control of ectoparasite infestations in equids. J Vet Pharmacol Therapeut. 2020. View Summary
  10. Pearson, W. et al. Association of maximum voluntary dietary intake of freeze-dried garlic with Heinz body anemia in horses. Am J Vet Res. 2005. View Summary
  11. O’Neill, W. et al. Flaxseed (Linum usitatissimum) supplementation associated with reduced skin test lesional area in horses with Culicoides hypersensitivity. Can J Vet Res. 2002. View Summary