Most horses in the USA are infested with 1 to 3 different species of Bot Fly (Gastrophilus intestinalis; G.nasalis; G.haemorrhoidalis) at some time during the year. All species penetrate the soft tissue of the horses’ mouth where they spend approximately 3 weeks. This can cause pain and irritation to your horses mouth and you might notice them rubbing the area. From there, they migrate to the stomach or small intestine where they attach and feed for several months. When conditions are right, they detach and pass out with the manure. Pupation takes place usually in the top layer of soil under the manure pile. Adults emerge 2 weeks to 2 months later then repeat this process.

 
Effective Bot Fly control is rather simple and can be manage with a good fall, mectin based, worming schedule to kill any ingested bot flies. For a non-chemical approach try removing the bot eggs every few days with a warm (110F) wet cloth or a pumice stone. The warm cloth will stimulate them to hatch and is the most effective method to remove them from your horse’s coat.
 
You can learn more about other types of flies on the Spalding Labs website here.