This study examines inter-operational taxonomic unit (OTU) relationships within a morphologically defined species complex of the African water rat Dasymys rufulus that comprises West, North, Central, and East African populations. Based on both traditional skull measurements and skull coordinates, 5 possible cryptic species within the rufulus complex were identified: western West Africa (Senegal to western-southeastern Ivory Coast), eastern West Africa (eastern-southeastern Ivory Coast to Nigeria, Chad), Central Africa (Cameroon, Congo, Democratic Republic of Congo), Central and East Africa (northern Angola, Zambia, southern Malawi, western Mozambique, Sudan) and southern Central and East Africa (southern Tanzania, northern Malawi, Mozambique). Data also confirmed that 2 recently identified species, D. foxi (restricted to Jos Plateau, Nigeria) and D. longipilosus (restricted to Mt Cameroon, Cameroon) are morphologically distinct. Each of the 3 datasets provided similar results, but the ventral skull coordinates were the most useful in separating OTUs with respect to a broad geographic pattern.