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This research was carried out in Usmanu Danfrodiyo University, Sokoto, to establish genotypic variations between C. gariepinus from two ecotypes (cultured and wild), using SDS-PAGE. Ninety (90) live samples of C. gariepinus were collected from three fish habitats, 30 samples from each ecotype were determined. The positions of the proteins were determined using ColorPlus Prestained Protein Marker, Broad Range (7-175 kDa). Bands were presented in increasing order of alphabets, following increasing order of molecular weight of the bands. The results revealed genotypic variations between the ecotypes. Conclusively, there was significant difference (P<0.05) between the genotypes of the wild and cultured C. gariepinus populations studied. The wild C. gariepinus population group from river Rima can be proteotypically (genetically) differentiated by the absence of allele B, and G while the cultured C. gariepinus from Magatakada farms can be distinguished by absence of allele E across the populations’ banding profiles. This finding presents baseline genetic information for further research and proper management of C. gariepinus from these water bodies.