This article is part of our Fly Control Awareness Month brought to you by Absorbine.

Flies and mosquitoes are more than just irritating barn pests that can ruin a peaceful ride. These pesky critters can also pose serious health risks to your horse. The insects act as carriers for dangerous diseases, spreading viruses through bites and exposure to body fluids. As a horse owner, it’s important to know about insect-borne disease, and how this can impact your horse. Knowing what illnesses flies and mosquitoes carry, and how to protect against them is key to keeping your horse healthy, especially during fly season.

Summer brings warm weather, longer days, more ride time…and flies. And flies can bring disease. Learn what to watch for, and how to beat fly-borne illness. ccestep8/adobe.stock.com
Mosquito-Borne Disease
There are three main viral diseases that can be transmitted to your horse by a mosquito: eastern equine encephalomyelitis (EEE), western equine encephalomyelitis (WEE), and West Nile virus (WNV). These may not be diseases you think about—you may not even realize they’re serious threats to your horse’s life. Yet they’re three of only five diseases that the American Association of Equine Practitioners recommends targeting with an annual vaccination for your horse.
Fly-Borne Disease
While mosquitoes are well-known disease carriers, flies and gnats also play a serious role in spreading harmful viruses and triggering painful allergic reactions in horses. Strangles is just one of many diseases that flies can transmit. Other fly-borne issues range from fly-bite allergies, conjunctivitis, and local irritation to life-threatening viral diseases like equine infectious anemia.
Equine Infectious Anemia (EIA)
Also known as “swamp fever,” EIA is a highly fatal viral disease primarily spread through the bites of horse flies and deer flies. These flies can transmit the virus if they’re interrupted mid-bite—such as by a swishing tail—and then move on to another horse. EIA can also spread through contaminated blood products or improperly sterilized equipment like needles, syringes, IV tubing, or tattoo tools.
EIA is unfortunately a high fatal disease spread through the bites of horse flies and deer flies. Grubärin/adobe.stock.com

Horses that survive the initial infection may become non-symptomatic carriers. They may appear healthy while still capable of spreading the disease. Symptoms include recurring fever, lethargy, loss of appetite, anemia, and low platelet counts. Preventing EIA outbreaks starts with routine testing. A negative Coggins or ELISA test is typically required annually for horses that travel or show, and in some states, testing is needed every six months.
Vesicular Stomatitis
VSV is spread by insect vectors such as black flies, sand flies, and midges, but it can also be passed between horses through direct contact with infected saliva, water buckets, feed, or contaminated equipment and clothing. Black flies most typically transmit the virus. When the fly population starts to swell, the disease starts transmitting. The flies that carry the virus are often found around water—outbreaks seem to occur closer to rivers or other bodies of water. There’s some speculation that mosquitos may also carry the virus.
The best protection against VS? Fly control. The only way to prevent the virus is meticulous fly control—fly sheets, fly masks, fly spray, manure removal, etc. Taking general biosecurity measures will also help prevent the spread of the virus. Currently there’s no vaccine.
Sweet Itch (Insect Bite Hypersensitivity or IBH)
This allergic reaction, also called Queensland’s itch, is triggered by the bite of the Culicoides midge (often referred to as “no-see-ums”). Though the midges typically bite on the horse’s belly, the allergic response becomes systemic, leading to intense itching.
In short, sweet itch is itchiness and results from stimulation of special nerve endings and receptors in the skin. Sweet itch also can develop with a combination of bites or conditions. With insect bites, it’s usually not the bite itself that causes the problem but rather an allergic reaction to the saliva. Horses will rub themselves raw on any available surface, often losing patches of mane, tail, and hair on the face, chest, and rump. In severe cases, horses may also show signs of respiratory distress.
Pigeon Fever
Pigeon Fever is transmitted to horses by house flies, stable flies, and horn flies—especially when these flies bite or land on open sores. The bacteria can enter the body through broken skin or be injected by the fly’s mouthparts during feeding. Once infected, a horse may develop painful external abscesses, internal abscesses, or ulcerative lymphangitis, which leads to significant swelling and infection of the limbs. The condition gets its name from the characteristic chest abscesses that resemble a pigeon’s breast.
Again, the best protection from Pigeon Fever is fly protection and fly control. Read on to find our best tips on managing flies to protect your horse from fly-borne diseases.
Fly Management Strategies
Below we’ve compiled some of our best tips for fly management and fly control. Your climate, weather, and barn setup will all play a role in determining your fly control strategy, so consider those factors.
The Basics
When it comes to fly control, here are your basic defenses to hold the line against these pesky creatures this summer.
- Remove that manure. Houseflies, your horses’ most common fly pest, are drawn to fresh droppings. This is where they prefer to mate and lay eggs; the resulting larvae feast on the feces. To keep that from happening, clean your horses’ stalls and pens daily, removing the manure to an off-site location once a week if possible, or covering the pile with a heavy tarp for later removal.
- Minimize moisture. Several fly species prefer wet areas for breeding as well as drinking. Keep stalls dry; eliminate standing puddles around your horses’ living areas; get rid of inadvertent water receptacles—old tires, no-longer-used buckets and feeders, etc.
- Cover consumables. Place all fly-attracting garbage in containers with bug-proof lids; keep grains, concentrates, and treats securely stored.
- Offer shade, air. A breezy, shaded area will help your pastured horses avoid flies; for stabled equines, barn fans are great fly-chasers.
Clean, Clean, Clean it Up
Flies thrive in dirty environments, so reducing breeding grounds before flies even have a chance to hatch, is key to effective fly control. Start by cleaning stalls, pastures, and paddocks. Regular manure management can significantly cut down fly populations before they start. If your horses stay in stalls or runs, cleaning them at least once a day will significantly reduce the amount of flies that are in or near the barn.
Find the Right Fly Spray
Fly repellants can be very effective. Studies have shown that resistance to insecticides used for controlling flies is highly variable depending on geographic location and the specific populations of flies. This means trial-and-error is probably the most effective strategy to help you determine if a fly repellent is working for your horse.
And be aware: A fly spray that works great at home might be less effective when you’re away from home, due to location-based resistance. Most importantly, the variable efficacy of fly repellants points out the need to have multiple weapons available for your War on Flies. no matter how hard to you try to eliminate breeding grounds and control populations, where there are horses, there will be flies.
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