It sounds like Raint Rot. If you are anywhere near the southern US like I am you have probably gotten a lot of nasty weather recently.
Rain Rot is pretty hard to treat in the winter. Your best bet is MTG, and making sure he's getting good feed. Might want to try some supplementing, like a regular multi-vitamin, or a Skin and Hair supplement.
In the warmer months you can wash him with an Iodine based shampoo and that will help. When you brush or curry be gentle as it does hurt them.
As it heals the hair WILL FALL OUT and then regrow. I simply spray the MTG and then as it starts falling out brush them to remove the hair.
Also you may want to check for scratches that would be on the backs of his heels, especially if he has white feet, for some reason they are usually worse. Scratches show up as nasty hard scabs with or with some swelling of the ankle. The scabs need to be removed as air is the only thing that will help kill the bacteria in there. If you are going to remove the scabs be sure to soften the first. Again the MTG works wonders, and usually the scabs wills simply fall off on their own.