The microchiropteran bat family Emballonuridae is widely distributed in archipelagos of the southwestern Pacific, with especially strong representation of genera Emballonura and Mosia. DNA sequences from three segments of the mitochondrial genome were collected from four species of Emballonura and from M. nigrescens to investigate the relationship of genetic differentiation to archipelago biogeography. Specimens of each species formed monophyletic clades in maximum parsimony and Bayesian analyses. Mosia nigrescens was genetically distant to the other four species. The other four studied species formed a monophyletic clade composed of the pairs E. beccarii, E. serii and E. raffrayana, E. semicaudata. Clades within species were strongly concordant with geography, with only two counterexamples (E. semicaudata in Fiji and E. raffrayana in the Solomon Islands) to the general finding that each island's population of a species constitutes a monophyletic clade. Genetic results do not agree with current subspecific designations within M. nigrescens. Samples from Woodlark, Alcester, and Manus Islands are phylogenetically closer to Papuan mainland samples than to Solomon Islands and New Ireland samples supposedly belonging to the same subspecies. Results suggest that Emballonura can establish populations across wide water barriers but does so infrequently. The isolating effect of water barriers is exemplified by the substantial genetic distinctiveness of Solomon Islands and New Ireland populations of both E. raffrayana and M. nigrescens. Absence from New Britain of E. beccarii, E. raffrayana, and E. serii (all known from New Ireland) may also reflect effects of water barriers if not due to collecting artifacts.