Horses are vulnerable to various fungal infections, but none of them affect the ears. What does sprout in the equine ear and is often mistakenly referred to as ear fungus is aural plaque. If you notice white flakes or build-up in the interior of your horse's ears, aural plaque is the likely culprit. If your horse lets your feel his ears and touch the plaque, it may seem hard because the affected skin has thickened. The skin pigment may permanently turn pinkish.
While aural plaque is primarily cosmetic, call your vet if your horse develops these growths. It's always possible that they could be melanomas or sarcomas -- tumors growing in the ears.
Flies a Vector
Aural plaque may appear in one or both ears. The condition is a response to the _papilloma viru_s -- which causes warts -- and is most likely spread to horses via black flies. The actual fly bite can cause pain to your horse, not the aural plaque itself.
Treating Aural Plaque
Your vet will likely advise you to just learn to live with the white stuff in your horse's ear, rather than try to treat it. That's because frequent handling of the ears can make horses ear or head-shy, as well as making the condition worse. If you can't live with aural plaque in your horse, your vet might prescribe an oil-based steroid cream to eradicate the plaque, but the ointment can cause discomfort to sensitive animals. The Merck Veterinary Manual reports that imiquimod cream, available over the counter, may get rid of aural plaques, but the drug causes "severe inflammation" and the horse may require sedation for topical application.
Preventing Aural Plaque
There's no surefire way to prevent aural plaque formation, but keeping your horse's inner ear hair intact helps a great deal. That's not possible if you show your horse, because neat, clipped ears are required in the show ring for many disciplines. If you must clip your horse's ears, put a fly mask on him that covers the ears to wear until the end of fly season. You can also rub fly repellent cream into his ears daily during fly season.