Evolutionary parallelism complicates taxonomy of the bat genus Scotophilus. This implies the necessity for a careful examination of morphologically similar species. Robbins' — or “nutlet” — house bat Scotophilus nucella is an insufficiently known taxon of the African rainforest zone based on just a handful of recorded specimens previously included in the nut-coloured house bat S. nux. Because its phylogenetic relationship to S. nux and other congeneric species is unknown, it was assessed using analysis of DNA sequences of single mitochondrial and nuclear genes. Based on the mitochondrial cytochrome b sequences, S. nucella was placed in sister position to S. nux. A genetic divergence of 7.8–9.4 % between them supports the recognition of S. nucella as a distinct species. Analysis of partial sequences of the nuclear zinc finger protein gene on the Y-chromosome corroborated the sister relationship of S. nucella and S. nux, while showing sufficient differences to consider them as two species. Mitochondrial genetic diversity in S. nucella was low, whereas S. nux showed a rather complex genetic structure over a large geographic area, despite limited sampling. The origin of the forest group of Scotophilus could be dated to the Miocene-Pliocene transition and the split leading to the contemporary species S. nucella and S. nux to the Pliocene-Pleistocene transition. Both time periods are characterized by an arid climate that led to the retreat of forest environment, which likely promoted speciation in forest refugia. Mid-Pleistocene diversification in S. nux led to a separate lineage from Guinea, West Africa, for which a subspecific status may be considered, as it differs 3.4–4.5 % from other African populations.