The endemic fauna of the Comoro Archipelago is composed of a mixture of taxa originating from Africa and Madagascar. Bats are the only native land dwelling mammals on this archipelago, but the biogeographical origins for the vast majority of species within this group are ambiguous. We report here genetic analyses based on two mitochondrial DNA markers to infer the origin of Comorian bats belonging to a reputed species complex of Miniopterus that is further distributed across Africa and Madagascar. Phylogenetic reconstructions show that east African M. minor are not closely related to the insular Miniopterus of Madagascar and the Comoros (Grande Comore and Anjouan). The latter cluster into two distinct, monophyletic clades (Clade 1 and Clade 2). Representatives of these clades occur sympatrically both on the Comoros and on Madagascar, and are distinguished by a large genetic distance (K2P: 9.9% for cytochrome b). No haplotypes are shared between any islands, suggesting the absence of contemporary gene flow. Populations of the widespread Clade 1 are furthermore characterized by a significant inter-island structure (Phi(CT) = 0.249), and by high haplotype and nucleotide diversities (h = 0.90-0.98, pi = 0.04-0.06). Demographic analyses of Clade 1 suggest secondary contact between two distinct phylogroups (Subclade 1 A and 1B) that reached Grande Comore and Anjouan, and a large, stable population with a long evolutionary history on Madagascar. These results and the current distribution of related lineages suggest that the Comoros were colonized independently at least two or three times by ancestors from Madagascar.