The family of sheath-tailed bats (Emballonuridae) constitutes a considerable part of the bat fauna of the Middle East. This region on the crossroad of three biogeographical realms represents the sole significant extension of the family range into the Palaearctic, otherwise the family is distributed mostly in the tropics. Three emballonurid species occur in the Middle East, Coleura afra, Taphozous perforatus and T. nudiventris, each with a number of morphology-based subspecies reported from the region. For this study, we assembled a dataset of more than hundred samples that covers the Middle Eastern parts of the ranges of the respective species. We generated sequences of up to three mitochondrial and five nuclear markers and reconstructed a time-calibrated phylogeny of the family to infer the evolutionary history of emballonurids in the Middle East and to revise their intra- and interspecific taxonomy. The populations of Coleura from southern Arabia and the Red Sea coast of Africa show a low genetic structure, although as a lineage are well separated from other Coleura populations of Africa and the Indian Ocean islands. We suggest this Afro-Arabian lineage to represent a separate taxon which could be regarded as a species of its own, C. gallarum. Similarly, low genetic structure across the study area we revealed in T. perforatus; this indicates that only one taxon of this bat is present in the Middle East and adjacent areas that should be co-identified with the nominotypical form. On the contrary, T. nudiventris presents two clearly separated clades; one of them comprises the nominotypical form of north-eastern Africa and southern Arabia, as well as the eastern Arabian populations assigned to T. n. zayidi, which is thus unjustified, and the latter name to be considered a junior synonym of T. n. nudiventris. On the other hand, the analysis did not resolve satisfactorily the phylogenetic position of the large body-sized Mesopotamian populations of T. nudiventris, which thus remains to be regarded as a subspecies T. n. magnus. Finally, the position of Liponycteris as a separate subgenus of Taphozous was not found to be justified, while the traditional divisions of the family into the subfamilies Taphozoinae and Emballonurinae and the latter into the tribes Emballonurini and Diclidurini were supported by the analysis results.