House flies, Musca domestica L., and stable flies, Stomoxys calcitrans (L.), are common pests in livestock, poultry, and equine facilities. Biological control of these 'filth flies' with pupal parasitoids can be used in conjunction with other control methods as part of an integrated fly management program. The principal filth fly parasitoids include members of the genera Muscidifurax and Spalangia in the hymenopteran family Pteromalidae, as well as others in the family Encyrtidae. Many of these parasitoids are native globally and have been introduced in many areas worldwide. Filth fly parasitoids are generally present in all habitats where suitable hosts can be found, including those associated with poultry, cattle, equine, swine, and other animal operations. They are also commonly occurring in refuse and forensic situations. Naturally occurring populations of parasitoids are typically insufficient to manage fly populations because of the flies' shorter development time and higher fecundity. Augmentation of natural parasitoid populations by releasing commercially-produced parasitoids can increase fly control. Here we review the biology of these biological control agents, and discuss the prospects for their successful use in managing filth fly populations in a variety of animal facilities.