Homology of male genitalic structures in the lower Brachycera is examined and implications for the phylogenetic relationships of the included families are discussed in light of other characters. The following character states belong to the ground plan of the Brachycera: the aedeagus is enclosed in a parameral sheath; the sperm pump possesses paired articulated lateral sclerites, and a large ejaculatory apodeme with a terminal endoaedeagal process; the epandrium and hypandrium are separate; the hypandrium is separate from the gonocoxites; and the gonostyli articulate and move in the horizontal plane. The placement of Heterostomus in Xylophagomorpha is supported, based on modifications of the sperm pump. The presence ofaedeagal tines suggests that Bolbomyia, which is currently placed in the Rhagionidae, may be more closely related to Athericidae + Tabanidae. The expanded first segment of the female cercus supports the monophyly of the Tabanomorpha, including Vermileonidae. The transfer of the Pantophthalmidae to the Stratiomyomorpha is confirmed on the basis of modifications of the sperm pump. The Stratiomyomorpha is hypothesized to be the sister group of the Muscomorpha (sensu Woodley 1989) based on the apomorphic development of a composite structure termed the phallus. The monophyly of the Muscomorpha is supported by gonostyli that articulate and move obliquely or dorsoventrally. The presence of acanthophorites in females is considered apomorphic for the Heterodactyla (Bombyliidae + Asiloidea + Eremoneura). Bombyliidae (exclusive of Mythicomyiinae and Heterotropus) is defined on the basis of reduced gonocoxal apodemes. Gonostyli retracted to a subapical position and a hinged larval metacephalic rod are considered apomorphic for the Asiloidea (exclusive of Bombyliidae) + Eremoneura. Hilarimorpha and Apystomyia are removed from the Bombyliidae based on the subapical placement of the gonostyli, and together with Apsilocephala are placed as incertae sedis in Therevidae. Apiocera is considered the sister group to the remaining apiocerids + Mydidae on the basis of absence of gonostyli and lateral ejaculatory processes in the latter lineage.