African mole-rats of the family Bathyergidae are subterranean hystricomorph rodents found throughout sub-Saharan Africa, where the distributional ranges of the most speciose taxa are divided by the African Rift Valley. In particular, mole-rats of the genera Heliophobius and Fukomys are distributed widely, and their adaptive radiation appears to have been strongly influenced by the geological process of rifting. As a result, virtually all members of the genus Fukomys occur in locations west of the Rift Valley. However, a small number of isolated populations occur east of the Rift Valley in Tanzania, where Heliophobius is widespread and is the predominant bathyergid rodent. Phylogenetic analysis of mitochondrial cytochrome b sequences of previously unstudied Tanzanian mole-rats (genus Fukomys) and geographically adjacent populations strongly suggests that vicariance in the Western Rift Valley has subdivided populations of mole-rats and, together with climatic changes, played a role in the isolation of extralimital populations of Fukomys in Tanzania. Together with molecular clock-based estimates of divergence times, these results offer strong support for the hypothesis that the observed patterns of cladogenesis are consistent with tectonic activity in the ‘Mbeya triple junction’ and Rungwe volcanic province between Lakes Rukwa and Nyasa. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 337–352.