Homologies of male genitalic structures in the Eremoneura (Empidoidea + Cyclorrhapha) are examined and implications for the phylogenetic relationships of the included families are discussed in light of other characters. A revised epandrial hypothesis for the evolution of male genitalia within the Eremoneura is presented, based on comparison of male genitalic features throughout the Brachycera, and a periandrial hypothesis is rejected. Ground plan modifications of the genitalia of Eremoneura include complete sclerotization of the subepandrial membrane along its length to form a subepandrial sclerite, formation of bacilliform sclerites, loss of the lateral ejaculatory processes of the sperm pump, development of a deeply emarginate epandrium, and fusion of the hypandrium with the gonocoxites. Ground plan apomorphies of the Cyclorrhapha, including Opetiidae, consist of a sperm pump separated from the base of the phallus, circumversion of the genitalia, loss of the gonocoxal apodemes, and development of surstyli. The ground plan of the Empidoidea is characterized by the apomorphic loss of gonostyli, and the development of a sperm pump with a lever-like ejaculatory apodeme. Surstyli have developed independently in several lineages of Empidoidea, parallel to their development in Cyclorrhapha, as have losses of the gonocoxal apodemes. The above characters support the monophyly of the Eremoneura and also indicate that the Empidoidea and Cyclorrhapha are sister groups, as opposed to alternative hypotheses that suggest the Empidoidea is paraphyletic with respect to the Cyclorrhapha. The monophyly of Cyclorrhapha, exclusive of Opetiidae, is supported by the presence of a phallapodeme. The Lonchopteridae and Phoroidea are united partially on the basis of a similar reduction of pregenital sclerites in the male. The Phoroidea is characterized by the apomorphic loss of gonostyli and abdominal spiracle 7 in the male. The Syrphoidea and Schizophora are hypothesized to share a synapomorphic lever-like phallapodeme. The Syrphoidea is characterized by a right-side deflexion of the hypopygium, whereas the Schizophora possess gonostyli that are adducted against the hypandrium, and circumversion that is completed entirely within the puparium.