I live in Alabama and fruit flies are an epidemic during the summer unlike anything I've ever seen. Even though my apartment mate and I are very clean people, I have opened my cabinet before and found a bordello of fruits flies.
Get rid of whatever is attracting them and put out some traps. Equal parts apple cider vinegar and water with a drop of dish soap. They're attracted to the apple cider and the dish soap breaks the surface tension so they drown.
Or join the fruit fly zombie horde. Your choice.