The pteropodid fruit bat genus Eidolon is comprised of two extant species: E. dupreanum on Madagascar and E. helvum on the African mainland and offshore islands. Recent population genetic studies of E. helvum indicate widespread panmixia across the continent, although island populations off western Africa show genetic structure. Little is known about the genetic connectivity of E. dupreanum or the divergence time between these two sister species. We examine sequence data for one mitochondrial (cyt-b) and three nuclear regions (β-fib, RAG1, and RAG2) to assess population genetic structure within E. dupreanum and divergence between the two Eidolon spp. In addition, we characterize the demographic history of both taxa using coalescent-based methods. We find little evidence for population structure within E. dupreanum, and suggest that this reflects dispersal based on seasonal fruit availability and a preference for roosting sites in exposed rock outcrops. However, despite apparent panmixia in both Eidolon spp. and large dispersal distances reported in previous studies for E. helvum, these two taxa diverged in the mid-to-late Miocene. Both species are also characterized by population expansion and young, Pleistocene clade ages, although slower population growth in E. dupreanum is likely explained by its divergence via colonization from the mainland. Finally, we discuss the implications of population connectivity in E. dupreanum in the context of its potential role as a reservoir host for pathogens capable of infecting humans.