The study evaluated the genetic signatures of the fishes from the two populations and compared the pattern of differentiation of the two populations with a view to separating the species from the different populations into possible sub-species. Forty (40) specimens were collected from River Niger (Lokoja) and Asejire Resevoir. The DNA of the twenty (20) specimens from each population extracted from the muscle tissue using phenol-chloroform extraction (PCE) method was subjected to microsatellite DNA analysis. Seven (7) microsatellite markers (Cga01, Cga02, Cga03, Cga05, Cga06, Cga09 and Cga10) were used in the analysis. Microsatellite DNA analysis of the two populations revealed signifi cant differentiation between the two populations as shown by the high values of heterozygosity, low level of inbreeding and non-conformance to Hardy-Weinberg’s equilibrium. It is concluded from the study that microsatellite analysis showed a high potentiality for separation of the populations.