In the Mediterranean region, cryptic diversity of bats is common. As distinct genetic lineages should be managed independently for conservation, insight into bat phylogeography is important. The Maltese islands are located in the centre of the Mediterranean between North Africa and Sicily and are densely populated. At present, it is thought that at least seven species of bats are native, but phylogeographic affiliations remain largely unexplored. Therefore, we sequenced a ca. 540 bp fragment of the mitochondrial 16S rRNA gene from 23 bats, which were captured during the citizen-science project Akustika. We found two morphologically cryptic lineages common in North Africa, Plecotus gaisleri and a mainly North-African lineage of Hypsugo savii (named Hypsugo cf. darwinii in some recent studies). We also recorded two Pipistrellus species. The P. kuhlii haplotype belonged to a lineage present in North-Africa and across the Mediterranean. Within P. pipistrellus we found two novel haplotypes that clustered within a North-African clade, well distinguished from the European haplotypes. Our results highlight the historic connection between the bat fauna of the Maltese Islands and North Africa. Malta is one of the few regions in the European Union where P. gaisleri and the North-African clades of P. pipistrellus and H. savii occur. Hence, Malta has an exceptionally high responsibility for the conservation of these taxa in Europe.