The Afrotropical leaf-nosed bat Hipposideros caffer has been traditionally regarded as a complex of populations, currently pertaining to two recognized cryptic species, H. caffer and H. ruber. Extent of distribution and morphological variation of these bats has raised concerns over whether the current perception of the complex reflects true phylogenetic relationships and taxonomic diversity. Our phylogenetic analysis of nucleotide sequences of the mitochondrial cytochrome b gene challenged the hypothesis of two cryptic species. Instead of the two reciprocally monophyletic lineages expected, corresponding to the two species, we recovered four distinct lineages with deep internal divergences. Two sister clades within a lineage of bats of H. caffer represent respectively the nominotypical form H. c. caffer, restricted to Southern Africa, and H. c. tephrus, inhabiting the Maghreb, West Africa and the Arabian Peninsula. Geographical isolation and deep genetic divergence suggest species status of both the forms. Another lineage comprises specimens of both morphotypes from West and East Africa. It probably represents a distinct species but its taxonomic assignation remains obscure. A Central African lineage of H. ruber comprises two sister clades, which become sympatric in Cameroon. Their status has to be clarified with additional evidence, since nuclear gene flow might be taking place. A further divergent lineage with H. ruber morphotype, most probably representing another distinct species, is restricted to West Africa. Although all three genetic forms of H. ruber may correspond to named taxa, their proper taxonomic assignation has to be assessed by comparison with type material.