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University of Minnesota Extension

Common flies around horses and how to control them

Quick facts

  • Control filth flies by managing moisture from manure, bedding, feed and mud.
  • Traps, stingless parasitic wasps and insecticides for filth flies are most effective when combined with debris management.
  • Managing water sources and providing your horse with deep shade or housing can best protect them from aquatic biting flies.
  • Work with a veterinarian to have your horse vaccinated for mosquito-transmitted viruses.
Horses express a few behaviors to remove flies, including rubbing their faces on their legs.

Flies are a natural part of keeping horses. Filth flies and aquatic biting flies are the main concerns in Minnesota.

Understanding these pests and how they live and breed can help horse owners limit their fly pest problems.

How do flies affect horses?

  • Transmit viruses and diseases.
  • Cause welts or skin irritation at bite sites.
  • Cause hoof damage from excessive stomping.
  • Cause overall discomfort as horses try to avoid them.

Horses usually swish their tails or stomp their feet to get flies to leave. They may also try to move their heads toward their bodies and limbs or twitch their skin to get rid of them.

How to best manage flies 

Mesh products like fly masks or leggings can help keep your horse more comfortable.
  • Keep your facilities clean and dry.
    • Remove manure and soiled bedding from horse areas often.
  • Use fly protectant products such as citronella spray, leg bands or leggings on your horses.
  • Provide a physical barrier between your horse and flies.
    • Use nets and screens on your barn doors and windows.
    • Use fly sheets and masks on your horses.
  • Use residual premise sprays where flies perch (barn walls and ceilings).

Filth flies

Filth flies develop in moist organic debris such as:

  • Aging feces
  • Soiled animal bedding
  • Rotting feed debris

Aquatic biting flies


Authors: Krishona Martinson, Extension equine specialist, Roger Moon, Betsy Wieland and Rachel Mottet

Reviewed in 2024

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