South African clinids are a major component of the temperate intertidal regions that are also known to participate in life cycles and transmission of several groups of parasites. However, the knowledge of trematode diversity of these fishes is incomplete. In this study, two species of Clinus Cuvier, the super klipfish Clinus superciliosus (Linnaeus) and the bluntnose klipfish Clinus cottoides Valenciennes, were collected from six localities along the South African coast and examined for the presence of trematodes. Metacercariae of Cardiocephaloides Sudarikov, 1959 were found in the eye vitreous humour and brain of C. superciliosus and in the eye vitreous humour of C. cottoides. Detailed analyses integrating morphological and molecular sequence data (28S rDNA, ITS2 rDNA-region, and COI mtDNA) revealed that these belong to two species, Cardiocephaloides physalis (Lutz, 1926) and an unknown species of Cardiocephaloides. This study provides the first report of clinid fishes serving as intermediate hosts for trematodes, reveals that the diversity of Cardiocephaloides in South Africa is higher than previously recorded, and highlights the need for further research to elucidate the life cycles of these trematode species. The broad geographical distribution of Cardiocephaloides spp. was confirmed in the present study based on molecular sequence data. The host-parasite interactions between clinid fishes and metacercariae of Cardiocephaloides are yet to be explored.