Two mitochondrial lineages of bats that are morphologically attributed to Hipposideros ruber have been shown to occur sympatrically in southeastern Senegal. We studied genetic diversity in these bats in the Niokolo Koba National Park using sequences of mitochondrial cytochrome b gene to determine the taxonomic status of the two genetic forms, and included skull morphology for comparison. Detailed multidimensional analysis of skull measurements indicated slight morphological differences between the two genetic forms. Exploration of peak frequency of the constant-frequency echolocation signals in a local population of Hipposideros aff. ruber was not available for both groups. Phylogenetic comparison with other available West African representatives of H. aff. ruber revealed paraphyletic relationship of the two Senegalese forms, with the less abundant form from Senegal forming a monophyletic group with that from Benin. Based on genetic divergence and sympatric occurrence, the two forms from Senegal might represent cryptic species. However, absence of nuclear gene flow between them is yet to be investigated to demonstrate their reproductive isolation.