The chiropteran family Myzopodidae is endemic to Madagascar and is characterized by several unique morphologies, such as sessile adhesive discs on the thumb and sole. A new species, Myzopoda schliemanni, was recently described from western Madagascar that is morphologically distinct and geographically disjunct from the eastern species, M. aurita, the only other member of this family. Geographic variation within Myzopoda has only recently been studied at the morphological level and has never been addressed at the genetic level. We used a combination of phylogenetic, coalescent, and population genetic analyses to characterize the speciation history of Myzopoda and to clarify current and former patterns of gene flow within and between Myzopoda. Mitochondrial DNA sequences were used to determine whether genetic data support the morphologically distinct species M. schliemanni, to infer the distribution of the common ancestor of extant Myzopoda, to estimate effective population sizes (N_e) and levels of migration between species, and to determine patterns of population structure within species. Phylogenetic and network analyses revealed the existence of 4 well-supported clades in Myzopoda, but could not resolve relationships among those clades. Divergent haplotypes within species may result from either recent gene flow between the 2 species or more likely from incomplete lineage sorting. Multiple coalescent-based methodologies produced concordant estimates of N_e for Myzopoda, but conflicting signals for migration between the species, probably reflecting differences in the underlying models used by the methods. We found significant genetic structure within M. aurita, but no correlation with geography. This pattern may result from recent gene flow facilitated by expansion of Ravenala stands, an important day-roost tree for Myzopoda, associated with anthropogenic deforestation and the opening up of new habitat for members of this genus.