The current study investigates phylogeographic structure of Zarhipis integripennis (LeConte) (Coleoptera: Phengodidae), a sexually dimorphic beetle with strongly asymmetrical dispersal abilities, to elucidate the spatial and temporal mechanisms of gene flow among populations in southern California. Using DNA sequences of a mitochondrial DNA marker and a nuclear intron in the krotzkopf verkehrt gene we compared the effect of differential dispersal on patterns of genetic structure among Z. integripennis populations across this area. Integrating these data with an ecological niche modeling analysis supported the hypothesis that dispersal between populations with fragmented niche availability was biased toward males and that female movement was limited and based on the availability of contiguous habitat. There was also evidence for historical restrictions to gene flow in the Sierra Pelona region of the Transverse Ranges based on a genetic break in both genes in this region.