The taxonomic status of the Turanian serotine Eptesicus serotinus turcomanus is still debatable. To examine the pattern of genetic variation in E. s. turcomanus and E. s. serotinus from SE Europe we analyzed sequence data on mitochondrial cytb gene and introns of THY and SPTBN genes. The cytb results do not reveal any substantial difference between E. s. turcomanus and E. s. serotinus from southern Russia. In contrast to that, the data on both nuclear genes indicate moderate differentiation between eastern and western populations and, at the same time, suggest the existence of gene flow between them. Several population history hypotheses can be proposed to explain the pattern. However, regardless of the scenario, our results demonstrate the lack of genetic isolation between E. s. serotinus and E. s. turcomanus and, therefore, contradict the species status for the latter.