We analyzed four morphological characters and a 307 bp fragment of the mitochondrial control region of the greater and lesser mouse-eared bats sampled in four colonies in Turkish Thrace and Anatolia. Bats were identified by reference to their upper toothrow length and rostral width. Despite a considerable variation in upper jaw measurements, there was not clear pattern relating the observed variability to particular regions. The genetic diversity of the mitochondrial control region was very high in the Thracian and Anatolian colonies (26 unique haplotypes in 82 sampled individuals), suggesting that these regions hosted one or more glacial refugia for M. myotis. The lesser and greater mouse-eared bats shared the same, or had very similar haplotypes. All haplotypes of the mitochondrial control region sampled in Thrace and Anatolia belonged to the haplogroup D. Haplotypes from the same group were previously found in the Balkans, Crimea, and Central Europe. The original mitochondrial lineage of M. blythii, reported from Kirghizstan, was not present in Anatolia. Apparently, in Europe, Central Anatolia, and Levant the greater and lesser mouse-eared bats have the mitochondrial genome of M. myotis.