The African sheath-tailed bat (Coleura afra, Emballonuridae) occurs patchily throughout sub-Saharan Africa and in southern Arabia. While the populations in southeastern Africa have been studied, those from the other parts of its distribution range have not been known well. We assessed genetic and morphological variation among some African and Arabian populations including those previously not studied. The recovered phylogenetic pattern suggests the existence of three major evolutionary lineages in this species. One lineage comprising populations from Kenya and Tanzania could be attributed to the nominotypical subspecies, although it surprisingly included also the population from Ghana. The respective populations from Yemen and Gabon were represented by the other two lineages. The recently discovered population of C. afra from Gabon shows considerable external morphological variation and a certain degree of sexual size dimorphism. Two morphogroups, based mainly on overall skull size, could be identified among populations from West Africa, East Africa, and Arabia. The larger-sized group corresponded to the nominotypical form. The smaller-sized group could be split into two subgroups defined by the skull shape, comprising populations from northeast Africa and Arabia, and West Africa, respectively. Although these two morphological subgroups seemed to correspond to forms gallarum/nilosa and kummeri, these allocations were not corroborated by the molecular analyses. Given the comparatively large genetic distances in C. afra, taxonomic revisions of the southern Arabian and Central African forms are anticipated.