The conservation of aquatic animal genetic resources is essential and necessary for effective breeding programmes. In this study, samples of Clarias gariepinus were obtained from different locations – Abeokuta, Ogun; Ile-Ife, Osun and Ikotun, Lagos States, for genetic relationships using Sodium Dodecyl Sulphate-Polyacylamide Gel Electrophoresis of their serum proteins with standard molecular marker. Results obtained showed varying sizes of polymorphic bands of the serum proteins including âgalactosidase, bovine serum albumin, ovalbumin, Carbonic anhydrase, and â-lactoglobulin. The similarity coefficients within the C. gariepinus were relatively high for Ile-Ife, Osun State (47%) and Ikotun, Lagos State (54%) compared with Abeokuta, Ogun State with highest value of 70%. The genetic relationship showed close relationship between strains from Lagos and Ile-Ife at genetic distance of 0.12 compared with Abeokuta at 0.31. This indicated a very high level of genetic similarity and general loss of genetic variation; hence, careful breeding programmes should be planned using breeding population with non-similar history but with unique features.