The airbreathing walking catfish (Clariidae:Clarias) comprises 32 species that are endemic to African freshwater systems. The species-level identification of this group is challenging due to their complex taxonomy and polymorphism. Prior to this study, the biological and ecological studies were restricted to a single species,Clarias gariepinus, resulting in a biased view of their genetic diversity in African waters. Here, we generated the 63-mitochondrial Cytochrome c oxidase subunit 1 (COI) gene sequences ofClarias camerunensisandClarias gariepinusfrom the Nyong River in Cameroon. BothC. camerunensisandC. gariepinusspecies maintained adequate intra-species (2.7% and 2.31%) and inter-species (6.9% to 16.8% and 11.4% to 15.1%) genetic distances with otherClariascongeners distributed in African and Asian/Southeast Asian drainages. The mtCOI sequences revealed 13 and 20 unique haplotypes ofC. camerunensisandC. gariepinus,respectively. The TCS networks revealed distinct haplotypes ofC. camerunensisand shared haplotypes ofC. gariepinusin African waters. The multiple species delimitation approaches (ABGD and PTP) revealed a total of 20 and 22 molecular operational taxonomic units (MOTUs), respectively. Among the twoClariasspecies examined, we found more than one MOTU inC. camerunensis, which is consistent with population structure and tree topology results. The phylogeny generated through Bayesian Inference analysis clearly separatedC. camerunensisandC. gariepinusfrom otherClariasspecies with high posterior probability supports. The present study elucidates the occurrence of possible cryptic diversity and allopatric speciation ofC. camerunensisin African drainages. Further, the present study confirms the reduced genetic diversity ofC. gariepinusacross its native and introduced range, which might have been induced by unscientific aquaculture practices. The study recommends a similar approach to the same and related species from different river basins to illuminate the true diversity ofClariasspecies in Africa and other countries.