In this study we analyzed 547 sequences of the first hypervariable domain of the control region of Miniopterus schreibersii sampled in colonies located in the western- and eastern-most borders of its distribution. We assessed genetic diversity of these colonies, quantified differences between them, and pointed out to their putative ancestral origin. Our results suggest that the extant European populations of M. schreibersii are descendants of the ancestors that survived the last glacial maximum in a single glacial refugium, probably located in the north-western Anatolia. According to our model, a rapid population expansion and major re-colonization events started after the climatic change that followed the end of the last glacial maximum. Our suggestions are supported by the shallow genetic differentiation between the eastern and western colonies of M. schreibersii, high genetic diversity observed in the eastern colonies, and population expansion time estimated for ca. 15.6 kyr BP.