Male-biased dispersal with female philopatry is a common pattern for many mammals. Because mtDNA is inherited maternally, biparentally inherited nuclear markers are often utilized to estimate population structure and gene flow. The pallid bat (Antrozous pallidus) exhibits a relatively continuous distribution across arid western North America. A previous mtDNA study suggested little gene flow among populations and identified three distinct phylogroups. We examined population structure of A. pallidus using amplified fragment length polymorphisms (AFLP) in 187 individuals from 29 localities across the distribution of the species. Eight primer pairs identified 797 polymorphic loci. All analyses indicated that populations in California, British Columbia, and the Baja Peninsula were relatively distinct. Cluster analysis indicated gene flow has been occurring between the Baja Peninsula population and populations to the north and east. The pallid bat appears to be characterized by male-mediated dispersal and gene flow, while females are largely philopatric. While several populations appear to be somewhat distinct, the overall pattern of divergence for A. pallidus is indicative of isolation by distance throughout the majority its range, suggesting significant gene flow has been occurring since populations diverged during Pliocene desert formation and mountain building.