A new species of Gyrodactylus is described from the gills of the near-threatened Clanwilliam sawfin, Cheilobarbus serra (Smiliogastrinae) collected from the Matjies River, Cape Fold Ecoregion, Western Cape Province, South Africa. Morphometry and morphology of the haptoral hard parts (hamuli, bars and marginal hooks) of Gyrodactylus serrai n. sp. differ from the other known species of the genus in the smaller size of hamuli and the shape and size of marginal hooks. Furthermore, ITS rDNA for the new species is unique among available Gyrodactylus spp. data in GenBank. Based on the uncorrected p-distances, G. serrai n. sp. is genetically most closely related to Gyrodactylus moroccensis Rahmouni, 2023 and Gyrodactylus pseudomoroccensis Rahmouni, 2023 from two species of Luciobarbus (Barbinae) from northern Africa, with interspecific divergence of 8.7% and 8.8%, respectively. The presence of a median ridge in the terminal part of the ventral bar membrane at G. serrai n. sp. most probably represents a morphological link to the North African Gyrodactylus spp. that suggests a morphogenetic association across the African continent as a result of ancient waterways that facilitated the dispersion of cyprinids and their parasite fauna or an independent evolution event retaining similarities from a common ancestor. The description of Gyrodactylus serrai n. sp. represents only the second species of Gyrodactylus described from an endemic South African cyprinid host, underscoring the need for focused research on this group of fishes to provide a sound understanding of the parasitic communities of these highly threatened and poorly studied hosts.