Macrogyrodactylus spp. from the gills of Clarias gariepinus in Zimbabwe and Kenya, and C. anguillaris in Senegal were identified using haptoral sclerite morphology and by sequencing the nuclear ribosomal DNA internal transcribed spacers (ITS) 1 and 2, partial 18S and the complete 5·8S rRNA gene. A molecular phylogeny was constructed using all sequenced Macrogyrodactylus species to date. Based on morphology, Macrogyrodactylus congolensis, M. heterobranchii, M. clarii, and M. karibae were identified, with one specimen from Zimbabwe displaying morphological features that were intermediate between M. heterobranchii and M. clarii. In the intermediate form, the partial 18S and ITS1 sequence was identical to that of M. clarii while the remaining ITS1 and complete ITS2 region was almost identical to M. heterobranchii as was the partial cox1 fragment, thus strongly suggesting a hybrid origin. At present, the catfish host of M. heterobranchii and M. clarii do not co-occur in southern Zimbabwe; this hybridization event is therefore proof of historical sympatry of both fish species.