Investigations into morphological and genetic differentiation of the potamonautid fauna of southern Africa revealed the presence of two morphotypes collected from the Drakensberg, KwaZulu-Natal. Both forms have been regarded as Potamonautes depressus in museum collections. The taxonomic status of the two forms was investigated genetically and morphometrically using samples from five localities. The two morphotypes could be distinguished on the basis of colour, with the northern morphotype being bright orange in colour, slightly smaller, and with a more thickly set carapace than the brown to green-brown southern morphotype. Allozyme electrophoresis utilizing 21 presumptive loci showed the two morphotypes to separate at a genetic identity value of 0.599. Five loci proved to be diagnostic between the two forms, with strong heterogeneity present at a further three loci. Discriminant functions analysis of seven carapace variables showed the two morphotypes to be morphometrically distinct. The southern morphotype was identified as Potamonautes depressus s. str., and it was concluded that the northern morphotype represented an undescribed species, described here as Potamonautes clarus sp. nov. The new species is compared to known Potamonautes species from South Africa.