The African rodent genus Saccostomus is common and widespread in the savannas, scrubby areas and cultivated fields from south Ethiopia and Somalia through East Africa down to the Cape Province. Its systematics and taxonomy are however poorly known, with two species currently recognized, S. mearnsi and S. campestris, the former is typical of the Somali–Maasai domain and the latter is typical of Zambezian–South African. The karyotypic findings and the analysis of the mitochondrial gene cytochrome b for some populations from Somalia, Tanzania, Zambia and South Africa are presented showing that the diversity within the genus is much higher than previously reported and believed, and that S. mearnsi and S. campestris rather represent species complexes, still actively speciating. The times of cladogenetic events and the extent of chromosomal variability within the genus that may be coupled with speciation are discussed. Finally, the possible taxonomy is considered in the context of the wide karyotypic variation shown by each species, the extent and the boundaries of which are still largely unknown, limiting therefore their definitive taxonomic assignment.