Flies and Horses – Oh, the Problems They Can Cause


Flies and horses don’t mix well, but you can do many things to keep your horse comfortable.  It’s about knowing what types of flies you are battling – and then creating a plan.


Table of Contents


How flies eat and transmit bacteria

Types of flies that affect horses

The problems that flies cause for horses 

Fly control measures

Shop for fly control supplies

Why flies are a nuisance for horses.


  • Flies are a nuisance for a few reasons – they are irritating and tickle and can sometimes be painful. They can also carry a myriad of diseases, as well as the potential to cause secondary issues. And, quite honestly, the lifestyle of a fly is really gross. To be perfectly scientific about it.


How flies eat and transmit bacteria and diseases.


  • Let’s get the super gross stuff out of the way first! If you casually eat your lunch and read this website for wonderful entertainment and knowledge, I greatly thank you! And also warn you to put your sammie down briefly as we discuss how most flies eat.



  • It starts with a puke. Some flies regurgitate saliva onto their food to dissolve it, which then allows the fly to drink his meal.


up close of a house fly
This is a puking machine that wears bacteria shoes. AKA a fly.


But how does a fly find his meal?


  • Some flies use their feet. YES – most flies taste things with their feet. Let’s take this one step further – most flies like to eat gross things, like manure and rotting things. This means that he will be covered in bacteria, and then he heads for your horse, where he will tap dance around until he finds something delicious to nibble on. Depositing his collection of leg grossness along the way.


  • Other types of flies in the horse fly category prefer to eat plant nectar and blood. The males and young females feast on plants. The females, however, need a blood meal to lay eggs. Horseflies, deer flies, greenhead flies, and their relatives will actually saw a hole in your horse and drink from the pool of blood. It’s painful and will leave a bloody mark on your friend.


  • Blood-drinking flies cause additional problems when a horse swats them away without finishing his meal. He may then find another victim and transmit diseases between animals.


The types of flies that affect horses.


House flies.


  • These little buttheads are the non-biting generic flies that populate barn and picnics alike. They feed on manure, trash, fruits, and picnic food. Their favorite egg-laying spots are warm, wet, and open – like your horse’s manure piles. A single female can lay 150 eggs about five times in her lifetime, and math tells me that’s a LOT of new flies.


  • House flies are seriously irritating to your horse and very often are the majority of fly that lives in your barn.



Third eye fly.


Stable fly.


  • These particular types of jerky insects will, indeed, bite your horse. They are extra-jerky in that they will also bite you, even through clothing. Fantastic. They also look a lot like houseflies.


  • Stable flies love to drink blood, and in this case, both sexes of the stable fly feed on blood. After a meal, they like to hang out on vertical surfaces. They also like your horse’s legs, another handy vertical surface. These are most commonly involved in the stomping reflex.


  • When eggs are laid, the larvae develop in wet areas – like urine-soaked bedding, wet compost, grass clippings, and water edges.


  • While it’s a good idea to use stinky fly traps, they are no match for the stable fly, which is not attractive to them.


Horse flies


  • Now let’s talk about the giant butthead flies out there. The Tabanidae family of flies includes deer flies, horse flies, and greenhead flies. They are typically larger than “regular flies” and the biggest “black bomber” horse flies are often 2 inches or so.


  • This family of fly feeds on blood. Their mouths have jaws that saw back and forth to get a blood meal – which is wickedly painful. Deer flies have a lovely habit of circling your head and dive-bombing you, which is why a common suggestion for hikers and outdoorsy types is to have a hat on with duct tape, sticky side up.


  • The larvae live in muddy, moist areas, like ponds and creek edges, so letting your horse graze in paddocks next to these areas may not work out so well.


  • There’s also the sheer size of these flies. It takes an obscene volume of fly repellent to do anything to deter these creatures from eating you and your horse if it does anything at all.


green head fly on a horse

This fly, about an inch long, makes a painful bite. It’s a greenhead and I despise them.


The horn fly.


  • These swarming flies usually like cows but will attack other species, including horses. They are small, about half the size of a housefly.


  • Horn flies love your horse’s back, but will use your horse as a rain shelter and attack bellies if the weather is bad. They also will snack on your horse about 30 times a day, relentlessly pursuing blood. For cattle, the incessant swarms can interfere with their milk production, and weight, and can even encourage self-harm.


  • Since these are mostly a cattle issue, your horse will likely be OK, but it’s something to watch out for if cows are in the area.


Black flies.


  • These are tiny little flies, and love ears! Sometimes they congregate around your horse’s neck, chest, and belly. They are usually in giant groups and are super annoying and irritating. They will bite your horse repeatedly, and cause crusty, bloody areas.


  • You can identify a black fly by the smaller size and the presence of a humpy back. Like some other blood-sucking flies, the males typically eat nectar, while the females drink blood to lay eggs. And shockingly, their eggs are laid near water. Most can be controlled with your typical horse fly sprays.



gnats in the sunlight

Gnats – I wouldn’t mind them so much if they tasted better.




  • Gnats are commonly called “no-see-ums”, which is pretty accurate. You may not see them, but you sure can feel them if you pass through a mass of them and accidentally eat and breathe a few.


  • Mostly, gnats are a nuisance and an annoyance. Some horses can develop sweet itch, which is a nasty allergic reaction to these near-invisible critters.


  • Gnats are also really tricky to control – and most often, you will need to use physical barriers like screens. Horses with sweet itch often need special sweet itch sheets and benefit from screen stalls at dawn and dusk.



Bot flies.



  • You may notice bot fly eggs on your horse’s legs or neck. They are tiny-looking seeds, often yellow in color. They end up in your horse’s mouth or nose when he rubs his body while self-grooming. Then it gets pretty gross.


  • It’s in your horse’s mouth that they hatch into larvae and burrow in his cheeks and tongue. They live there for a bit, then they migrate to his stomach and attach themselves there, also as larvae. Come springtime, the larvae are passed with your horse’s manure into the soil to pupate into adult flies.



yellow bot eggs on a horse knee

Bot fly eggs on a horse’s knee. SUPER STICKY.


Screwworm flies, blow flies, and warble flies.


  • These flies are also considered parasites, as they live off your horse. Screwworms and blow flies deposit eggs on wounds, and as the eggs hatch, the resulting maggots invade your horse’s tissue.


  • Warble flies have a different mechanism of parasitism. Eggs are laid directly on the skin, and the larvae burrow into the skin and then migrate to the back and esophagus. During warm weather, the larvae bubble up to the surface, creating tiny holes in your horse’s skin to breathe. These holes become escape routes to fall to the earth and continue their life cycle. Alternatively, the larvae will mineralize and create occult sarcoid tumors. Sometimes the warble fly larvae end up in your horse’s brain, causing death.


For help identifying the types of flies you find around your horse, these are good resources:




The problems with flies and horses.


  • At the very minimum, flies make life irritating and uncomfortable for most horses. Flies tickle as they creep along your horse, and some pack a bit of a punch as they chew on your horse. There’s tail swishing, belly kicking, neck swinging, and doing what they can to eliminate those pests.




  • It’s not uncommon for horses to stomp to rid their legs of flies. Stomping, while seemingly innocuous, can be problematic for a human in the wrong place at the wrong time. Horses can also loosen horseshoes, contributing to cracks and hoof issues with repeated stomping.

Summer sores


  • Habronema worms are a species of stomach worm that lives in horses. Their larvae are passed in your horse’s manure and flies then eat them.


  • When an infected fly lands on a cut, scrape, mucous membrane, eye area, genital area, or anal area, the introduction of the worm into that area causes a HUGE inflammatory response. A tiny cut can often open overnight into a seeping and oozing sore. This article has more information and some rather graphic photos for your perusal.


  • These sores can last months, are difficult to contain, and can even cause lameness if a wound on the leg occurs.




summer sore in the corner of a horse's mouth

A summer sore that’s almost healed.




  • Some horses are just plain allergic to flies. A horse might get welts, hives, itchy patches, or a full-blown case of sweet itch. Part of the problem with these cases is that the allergic response creates such itchiness, that some horses will scratch their skin off to relieve the itch. This can create a host of other issues, including secondary infections and healing issues.

Equine Infectious Anemia (EIA)


  • Equine Infectious Anemia is detected by the yearly Coggin’s test. The virus that causes this disease is transmitted by flies. Once a horse with EIA has been bitten, the virus is alive in the fly for about an hour. The disease will spread if he bit another horse in that time frame. This is why horses nearby are vulnerable to transmission.


  • EIA causes fever, anemia, abdominal swelling, leg swelling, weight loss, and muscle wasting. Organ damage, secondary infections, and death often follow. There is no cure, no treatment, and horses that develop EIA must be euthanized or permanently isolated from other horses.


Eye worms


  • Yes, there’s a worm that can infect your horse’s eye. Sometimes you can see it; sometimes you can’t. Flies transmit this worm, picking up larvae while they feed, and depositing them right back into your horse’s eye area.


  • You will usually see some swelling, and you may even see some worms near the tear glands, the third eyelid, and the cornea. Most horses with eye worms don’t show any signs at all. Of course, your vet is needed to pick these worms out.


Pigeon fever


  • This disease caused by bacteria transmitted by horn, stable, and house flies, creates swellings on your horse’s chest, puffing him up like a pigeon. Which is really a pus-filled abscess. Other variations of this disease involve lymphangitis of the legs and internal infections. Things can go sideways quickly, with recurrent abscesses, lamenesses, and fevers.


  • Flies carrying this bacteria, which also lives in the soil, mechanically transfer it to your horse via wounds or mucous membranes.


horse with large bug bits on her side

Fly bites can leave welts or hives on some horses.


Fly control – all stages of the life cycle


  • It’s rare to find a barn that has zero flies at all. It’s also impossible to find a fly control method that works for all stages of the fly life cycle, and for all types of flies. You need to attack all flies, from all angles, in all stages of the life cycle. You will also need to investigate what types of flies you have at your barn – as many of them require different traps to contain their populations.




  • Fly predators are often called beneficials, and are tiny wasps that take over fly cocoon, destroying the pupal stage of flies. These need to be released at regular intervals and be sure to avoid using sprays and other chemicals around them.


Fly sprays


  • Common fly sprays contain ingredients to knock down, kill, or deter flies. Chemicals such as pyrethrins, pyrethroids, and fatty acids work differently to help your horse stay fly-free. Many have a few hours of working time; others last longer. It’s handy to know what’s in your fly spray, so you can plan your management accordingly.


horse wearing a fly sheet that's too small

They only work if they fit.


Fly sheets and masks


  • These literal barriers make your horse mostly impervious to flies. Some flies are nasty buggers and will bite through the sheet. Some flies that naturally attack from below, like the greenhead, can often get stuck inside the sheet.


  • If your horse suffers from sweet itch, buy a sheet with a face and belly coverings and elastic closures around legs.

Fly boots and horse socks.


  • Stomping and summer sores can be greatly reduced with horse socks or fly boots. If your horse is prone to skin infections, equine pastern dermatitis, or summer sores on legs, go with socks. For stomping and fly irritation, fly boots should be just fine.


horse wearing sox for horses on mat

Yes, your horse can wear socks. These are Silver Whinny’s from Sox for Horses.


Selective turn out


  • Some horses can also greatly benefit from being stalled during heavy fly times of day. I currently live in an area where turnout is overnight in the summer and during the day in winter. My own horse will choose to stand in his shed under the fan during the day when he has free choice to be outside. The bugs are unreal.


  • Horses with sweet-itch can be stalled, with screens if possible, during dusk and dawn when the midges are most active.


Fly traps


  • Here’s where it gets specific to what type of fly you are battling.



  • There are also traps for the larger horseflies, usually involving giant black spheres. Like yoga ball size giant. You can cover the spheres with sticky glue; some have nets to funnel the flies into traps.


  • You can buy fly traps or you can make your own. Most homemade fly traps involve some sort of rotting food. Store-bought traps also have some sort of horrible smelling bait. Set these away from your barn, to save your nose and lure flies away.


  • For gnats, you are limited on options. Some gnats are attracted to fly sprays, especially those with essential oils. Some gnats will eagerly die in a solution of two tablespoons of vinegar and one tablespoon of sugar. Add to a liter of water, top it off with a few drops of dish detergent, and lure them away from the barn.


fly bag trap for barns


Deworming programs


  • Use a deworming program based on your vets recommendations and fecal egg counts. Combatting bot flies is often effective after a freeze, as the larvae use your horse to stay safe from cold weather. Deworming in the winter for these guys assures the life cycle is broken, as nothing will be passed in the spring.


  • For other types of worm issues, like eye worms and summer sores, your vet can help you decide what dewormer to use, how to use it, and when to use it.


  • Deworming is becoming less effective over time and varies greatly as to what parasites are actually in your horse as well as your horse’s environment and climate. Your vet is the best person to advise you on this.



Flies and horses will always be a challenge – this is only a place to start. Do get to know the types of flies in your area, and the best ways to defeat them. Sometimes it’s as simple as a trap, for other types of flies you need more than one approach.


go shopping button for horse products


GUYS! I put together this casual list of supplies to battle flies. As an Amazon Associate, I earn from qualifying purchases, and this is ZIPPO extra charge to you! Thank you for your support – this helps me keep the website floating along!

Fly predators!

This fly spray is weird but also great for certain types of flies

Fly traps, in case you want to buy them instead of making them.


A popular fly spray

Cashel Crusader Horse Fly Mask with Ears and Long Nose – select size


Cashel Quiet Ride Standard Horse Fly Mask with Ears for riding


Another style of long-nose fly mask for horses


How about some fringe?

                                                   This fly mask is also great for use under grazing muzzles to prevent rubs. 



Cashel Quiet Ride Bug Armor – 2 Piece Set

Amigo Mio Fly sheet – I love this one, the extra long tail prevents bugs up the butt, and the neckpiece is great. It’s also super light, which means it tears easily.

                                                                                     Zebra prints are said to confuse flies.


Thank you!

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