Due to a morphological uniformity typically shown by bent-winged bats, the taxonomic recognition of species and subspecies within the sole genus Miniopterus has been much questioned and revised. The situation and definition of the African species M. minor is particularly confused. This species is known from scattered and discontinuous records on both mainland coasts, Madagascar, São Tomé and Grand Comoro islands. The island forms have been included either within M. minor or considered as endemic species. To clarify their taxonomy, we compare mitochondrial DNA sequences of all the island forms with other related African Miniopterus. The genetic distances found in this study support a taxonomic recognition of the island forms at species level and the phylogenetic reconstructions based on these data suggest that the M. minor, as considered traditionally, is not a monophyletic group. The morphological similarities between the Miniopterus from São Tomé (West Africa) and Grand Comoro (East Africa) may reflect convergent evolution rather than a common ancestry.