This study determined the genetic variations that exist in Clarias gariepinus obtained from two natural populations in Nigeria, using their serum protein profi les. A total of 51 samples of Clarias gariepinus collected from Ado-Ekiti and Ilesa were used for this experiment. Blood was extracted from the caudal vein of each individual fi sh and electrophoresis was performed based on standard methods. Following this, gel images were taken, scored and subjected to classical cluster analysis using Bray-Curtis similarity index. This showed the presence of variations in C. gariepinus between the studied populations and samples from Ado-Ekiti reservoir displayed more diversity than those from Ilesa. Hence, this showed the feasibility for selecting samples from Ado- Ekiti to improve culture of C. gariepinus in further breeding studies.