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Pipistrellus deserti is a small, pale-coloured bat occurring in the most arid parts of the Sahara, in Morocco, Algeria, Libya, Egypt, and the Sudan, and marginally also in sub-Saharan Africa. Although most authors consider P. deserti as a full species, others regard it as a subspecies, or even as a junior synonym of Pipistrellus kuhlii. We analysed the topotype material of P. deserti from Libya using both morphologic and molecular characters, and compared them with samples from other Saharan countries and with P. kuhlii from around the Mediterranean. The Libyan samples of deserti are morphologically very similar to other populations from arid parts of North Africa (Morocco, Algeria, Egypt, Sudan), but differ markedly in the size of most skull dimensions when compared to P. kuhlii sampled in more mesic areas. However, phylogenetic reconstructions indicate that mitochondrial haplotypes of typical P. deserti from Libya and those from Morocco do not form a monophyletic group but are fully embedded within the larger radiation of P. kuhlii from Africa and Europe, rendering this species paraphyletic. Limited nuclear information (five microsatellite loci) also failed to provide evidence of significant differences between the two morphotypes, as pipistrelles are instead grouped by geographic origin. Altogether, these genetic data suggest that the morphological uniqueness of P. deserti may result from recent adaptations to arid habitats, rather than reflect a long independent evolutionary history. In the absence of more compelling evidence of barriers to gene flow, we therefore suggest Pipistrellus deserti to be considered a junior synonym of Vespertilio kuhlii (=P. kuhlii).