Instability characterizes the taxonomy of the African rodent subfamily Otomyinae. Two genera, Otomys and Parotomys, and 14 species are currently recognized, but the generic subdivision is equivocal. Between two and five cytotypes are delimited within O. irroratus, which illustrate a rapid rate of karyotypic evolution, and may reflect incipient speciation. In an attempt to resolve the group's phylogeny, the mitochondrial cyt b (complete) and 12S rRNA (802 bp) genes were analyzed using parsimony, distance and maximum likelihood methods. Alternative models of evolutionary change were compared to determine the best-fit model for each data set. Both genes failed to resolve deeper evolutionary associations, but the cyt b gene proved useful in resolving relationships among closely related taxa. Robust associations consistently retrieved include: (1) the O. irroratus cytotypes form a monophyletic group with O. laminatus basal. (2) an exclusively East African clade comprises two representatives of O. anchietae lacustris (not sister taxa), O. tropicalis with O. denti basal~ (3) Otomys angoniensis and O. maximus from southern Africa are monophyletic sister taxa with O. typus jacksoni and O. typus successively basal, making the East African Otomyinae non-monophyletic. (4) Parotomys brantsii and P. Wtledalei cluster within Otomys, but with no clear sister relationships. These results question some of the nomenclatural divisions in current use. First, the paraphyly of Otomys renders the recognition of two distinct genera unsupported. Second, the strongly supported monophyletic clustering of O. angoniensis and O. maximus coupled with the comparatively small genetic distance separating them, disputes the status of O. maximus. Third, the paraphyletic associations shown for representatives of O. typus and O. anchietae might imply that distinct evolutionary lineages are contained within these species. Otomys irroratus is phylogenetically distant from other Otomys species previously considered conspecifics. Moreover, a sister association between the Band C cytotypes to the exclusion of Al and A2, corroborate the delimitation of two major cytogenetic groups within O. irroratus. The major clades form an unresolved polytomy suggesting that the Otomyinae experienced a rapid radiation approximately 5 Myr ago. A biogeographical scenario is presented in light of palaeo-climatic changes during the late Miocene and Plio-Pleistocene epochs. / Thesis (DPhil (Zoology))--University of Pretoria, 2005. / Zoology and Entomology / unrestricted