The distribution of pipistrelles of the Pipistrellus pipistrellus complex (= P. pipistrellus s.l.) reaches only marginally the African continent. These bats are known only from a narrow belt of the Mediterranean zone in Maghreb and from NE Libya. We analysed museum specimens of African populations of P. pipistrellus s.l. using both morphologic and genetic techniques and compared them with Eurasian specimens of the complex. The African representatives of P. pipistrellus complex include two morphologically, genetically and geographically distinct populations. One of them inhabits the Mediterranean part of Cyrenaica, Libya. Belonging to the P. pygmaeus genetic lineage, these bats are represented by larger and more rusty coloured individuals with large massive rostrum and canines. In morphologic traits, this population differs significantly from all Western Palaearctic populations of the P. pipistrellus complex. These bats differ by about 6–7% in genetic distance from P. pygmaeus s. str. Within the P. pygmaeus lineage Libyan bats seem to be unique in their echolocation calls: the maximum energy of terminal frequencies was recorded at about 45 kHz. We consider the Libyan pipistrelles to represent a separate species, Pipistrellus hanaki sp. nov. Another distinct African pipistrelle population inhabits the Mediterranean parts of NW African countries, Morocco, Algeria and Tunisia. Individuals from the latter population are small and somewhat darker members of the P. pipistrellus genetic lineage, with relatively short and narrow mesial part of rostrum. Although both morphological and genetic differences between this population and Eurasian P. pipistrellus s. str. were found (genetic distance about 3–5%), they are probably not sufficient for the separation of this form at the specific level. However, the differences from European samples show rather not a cline character and therefore potential subspecific level of NW African P. pipistrellus has to be taken into consideration.