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The genus Natalina Pilsbry, 1893 is a southern African endemic belonging to the Gondwanan family of carnivorous snails, Rhytididae. We present a well-resolved molecular phylogeny of the genus based on the mitochondrial 16S and COI genes and the nuclear ITS2 gene, and assess this in light of Watson’s [Watson, H., 1934. Natalina and other South African snails. Proc. Malacol. Soc. Lond. 21, 150–193] supra-specific classification via a re-examination of 23 morphological characters including features of the shell, radula, external anatomy and distal reproductive tract. Ancestral reconstruction and character mapping based on the MK₁ model reveals broad concordance between morphology and the molecular phylogeny at the supra-specific level. Given this concordance and exceptionally deep divergences in the molecular data, we recommend the elevation of the subgenera Natalina s.s., Afrorhytida, and …