Zoologica Scripta, 2016We explore diversity of African pouched mice, genus Saccostomus (Rodentia, Nesomyidae), by sampling molecular and morphological variation across their continental-scale distribution in southern and eastern African savannahs and woodlands. Both mitochondrial (cytochrome b) and nuclear DNA (IRBP, RAG1) as well as skull morphology confirm the distinction between two recognized species, S. campestris and S. mearnsi, with disjunct distribution in the Zambezian and Somali–Maasai bioregions, respectively. Molecular dating suggests the divergence of these taxa occurred in the Early Pliocene, 3.9 Ma before present, whereas the deepest divergences within each of them are only as old as 2.0 Ma for S. mearnsi and 1.4 Ma for S. campestris. Based on cytochrome b phylogeny, we defined five clades (three within S. campestris, two in S. mearnsi) whose species status was considered in the light of nuclear DNA markers and morphology. We conclude that S. campestris group consists of two subspecies S. campestris campestris (Peters, 1846; comprising two cytochrome b clades) and S. campestris mashonae (de Winton, 1897) that are moderately differentiated, albeit distinct in IRBP and skull form. They likely hybridize to a limited extent along the Kafue–Zambezi Rivers. Saccostomus mearnsi group consists of two species, S. mearnsi (Heller, 1910) and S. umbriventer (Miller, 1910), that are markedly differentiated in both nuclear markers and skull form and may possibly co-occur in south-western Kenya and north-eastern Tanzania. Analysis of historical demography suggests both subspecies of S. campestris experienced population expansion dated to the Last Glacial. In the present range of S. campestris group, the distribution modelling suggests a moderate fragmentation of suitable habitats during the last glacial cycle, whereas in the range of S. mearnsi group it predicts substantial shifts of its occurrence in the same period.