Filth flies (Diptera: Muscidae), particularly the house fly, Musca domestica L., are global pests of livestock production. In this study, we characterized the fauna of house fly pupal parasitoids in Israel and identified factors affecting their diversity and abundance. The study, which included one round of sampling during the fall of 2013 and another round of sampling in the spring of 2014, encompassed 26 locations of common fly-breeding habitats: dairy, egg-laying, and goat farms throughout Israel. Nine parasitoid species were found: Spalangia cameroni Perkins, Spalangia endius Walker, Spalangia drosophilae Ashmead, Spalangia gemina Boucek, Spalangia nigroaenea Curtis, Pachycrepoideus vindemmiae Rondani, Muscidifurax raptor Girault and Sanders, Muscidifurax zaraptor Kogan & Legner (all Hymenoptera: Pteromalidae), and Dirhinus giffardii Silvestri (Hymenoptera: Chalcididae). This is the first record of S. gemina from the Palearctic, as well as the first record of S. drosophilae from the Middle East. The composition and relative abundance of parasitoid species varied markedly among localities, climatic regions (Mediterranean vs. desert), habitat types (dairy vs. egg-laying vs. goat farm), and seasons. Overall, parasitoid richness in egg-laying farms was two- and sevenfold higher than in dairy and goat farms, respectively, and three times higher in Mediterranean than desert climate. The significance and implications of our results for inundative biological control programs of filth flies are discussed.