Gyrodactylus sprostonae Ling, 1962 is a highly invasive parasite reported across freshwater environments of the northern hemisphere. The taxon was originally described from Carassius auratus (Linnaeus, 1758) and Cyprinus carpio Linnaeus, 1758 in China. This parasite has never been reported in Africa or the southern hemisphere. Recently, this taxon was collected from an indigenous yellowfish, Labeobarbus aeneus (Burchell, 1822), in the Vaal River, South Africa. The present study includes the conclusive identification of the gyrodactylid parasites collected from L. aeneus, including additional taxonomic data, using microscopy and molecular techniques. Microscopy included light microscopy (LM) of whole worms and scanning electron microscopy (SEM) of isolated haptoral sclerites. Additionally, morphometric data were obtained from SEM and compared to that generated using LM. For molecular analysis, the internal transcribed spacer (ITS) region of rDNA was amplified and phylogenetic topologies constructed. The specimens were morphometrically and genetically highly similar to other data for G. sprostonae. Additional point-to-point measurements and ITS rDNA sequences were generated for the taxon, contributing to the morphometric and molecular data for G. sprostonae. The study also includes the first study of the isolated haptoral sclerites of the taxon using SEM, with similar morphometric results to LM. This is the first record of G. sprostonae in the southern hemisphere and from a new, indigenous African host, L. aeneus, indicating host switching to smallmouth yellowfish. Furthermore, these results expand on the knowledge of the distribution of invasive parasites in South Africa, as well as Gyrodactylus species diversity in Africa.