Museum specimens of African populations of P. pipistrellus sensu lato were analysed using both morphologic and genetic techniques and compared with Eurasian specimens of the complex. Two morphologically, genetically and geographically distinct populations were found. One of them inhabits the Mediterranean part of Cyrenaica, Libya. This population differs significantly from all Western Palaearctic populations of the P. pipistrellus complex and has been described as a new species, Pipistrellus hanaki. Another distinct African pipistrelle population inhabits the Mediterranean parts of NW African countries, Morocco, Algeria and Tunisia. Although both morphological and genetic differences between this population and Eurasian P. pipistrellus were found, they are probably not sufficient for the separation of this form at the species level.