In this study we investigate population genetic structure and phylogeography of the bent-wing bat complex (Miniopterus schreibersii) in Asia Minor and adjacent regions. PCR amplification and sequencing of the first hypervariable domain of the mitochondrial control region were used to obtain the genetic data. Morphometric differentiation between lineages was analysed by comparing forearm lengths. We found two reciprocally monophyletic lineages within the M. schreibersii complex, identified as M. s. schreibersii and M. s. pallidus. Distributions of the lineages were allopatric with a U-shaped suture zone passing through Central Anatolia. The suture zone separated coastal regions occupied by M. s. schreibersii from inland, higher altitude regions occupied by M. s. pallidus. The lineages showed a considerable sequence divergence of c. 9%, accompanied by a corresponding difference in forearm length. The presence of the genetically distinct lineages, with allopatric distribution and corresponding morphometric differences, probably reflects their long isolation during the ice-age in the Balkans and the Caspian/Caucasus refugia, followed subsequently by expansion into different habitats. Based on the present data, the lineages can be recognized as evolutionary significant units.