Resolving species limits within the genus Miniopterus has traditionally been complicated by the presence of cryptic species with overlapping morphological features. We use molecular techniques, cranio-dental characters and tragus shape to describe a new species of Miniopterus from Mozambique, M. mossambicus. Miniopterus mossambicus shows > 12% divergence in cytochrome-b sequence from its nearest congeners (the Malagasy M. gleni and M. griveaudi) and > 15% divergence from the morphologically similar M. natalensis, M. fraterculus and M. minor (all of which occur in southern and eastern Africa). There is considerable overlap in cranio-dental characters of the southern African species, particularly M. natalensis and M. mossambicus. However, tragus shape and multivariate comparisons of skull measurements can be used to separate these species. Based on morphological comparisons of museum specimens, this species may also be present in neighbouring Malawi and Zimbabwe, suggesting that it is probably distributed widely in south-central Africa.