Wild Clarias fish species are used for aquaculture in Cameroon, but information on their characterization is limited and mislabelling is rife. The purpose of this study was therefore to characterize wild and cultured Clarias fish specimens from Cameroon. Twenty-six (26) morphometric features, 3 meristic counts, some morphological observations and the cytochrome oxidase subunit I (COI) gene were used for the characterization. Based on gill raker count (GRC), specimens were separated into two principal groups. One group was tentatively identified as C. gariepinus and the second group as C. jaensis. However, because of the discrepancy in pectoral spines serration, the second group was referred to as C. aff. jaensis. Clarias gariepinus from Nkam and Mezam Rivers possessed the crescent vomerine while the cultured stock had interrupted vomerine and those from the Mungo River had both forms of vomerine. Based on phylogenetic tree, C. gariepinus from Mungo River was more diverse and ancestral compared to the other populations. Genetic identity of C. aff. jaensis with GenBank references was 92-94%. So the exact identity of the species remained unclear. Further studies are therefore needed to determine if these sequences represent an isolated branch of C. jaensis or if they belong to another species.