If its a sever case ( whole backline) bath them with betadine scrub , use a medium bristled brush and scrub off as many of the scabs as you can and let the horse dry , spray the horses back (with 3capfulls of bleach and the rest water in a spraybottle). Do that every other day for a week and the horse will loose all the hair where the rain rot has occured, after you have scrubbed all the scabs off of the horse, when you wash with the bettadine, rinse the horse off and then rub some more bedadine on the horse do not rinse it off, the bleach water helps kill the fungus and the betadine keeps it down. Horses can get rainrot sittin in a stall out of the weather, the way I had it explained to me by a vet at a&m is that its a fungs that strives on moisture. The reason why they call it rain rot is the pattern of the scabs looks like the pattern of rain running down the horses back, if you simply brush your horse every day when you feed it will keep the bacteria down and shouldnt come back. If it does just give them a good betadine scrub bath. I've used it on my 10 yr old mare. And it took 2 weeks to get rid of all the scabs and kill the fungus but took a good month to get all the hair back.