The freshwater fish fauna of southern Africa is highly diverse; however, the magnitude of parasitic species they host is unevenly known. The region’s documented adult trematode fish fauna is sparse, while the opposite is evident for intermediate trematode stages. Perceived difficulty in identification of underdeveloped stages lead to the exclusion of reporting metacercariae or lack either morphological or molecular data resulting in a depauperate comparative molecular data repository for species of the region and Africa as a whole. In an effort to address the morphological and molecular data void of the parasite fauna of southern African freshwater fishes, we sought to comprehensively investigate and characterise this fauna. Here we report on three metacercarial forms of Clinostomum (Clinostomidae) from three fish families (Clariidae, Mochokidae, and Mormyridae), provide the first report of a species of the Cryptogonimidae from a cyprinid host in South Africa, and include molecular data for the partial 28S rDNA, ITS1–2 and COI mtDNA regions of these metacercarial forms. Our clinostomid specimens morphologically and genetically corresponded with Clinostomum brieni (e.g., Clarias gariepinus) and Clinostomum ‘morphotype 2’ and ‘morphotype 3’ per Caffara et al. (2017) from the mormyrid Marcusenius pongolensis and the mochokid catfish Chiloglanis sp., respectively. Our cryptogonimid metacercariae did not correspond with any known species or available molecular sequence data; however, the presence of robust circumoral spines on the oral sucker indicated that they are either a species of Acanthostomum or Proctocaecum. The molecular data we provide are the first for an Acanthostomum/Proctocaecum-type cryptogonimid from Africa.