Genetic signature of some Egyptian populations of the fish Hemichromis bimaculatus was detected using some isozyme systems including: Malate dehydrogenase (Mdh), Malic enzyme (ME), Esterase (Est) with three specific esterase substrates and protein polymorphisms. The applied samples were obtained from three distantly Egyptian locations namely, Qariater (Q population), Wadi EL-Rian (R population) and Lake Manzala (Ml and M2 populations). The samples were extracted from skeletal muscles. Native PAGE (10% polyacrylamide gel under non denaturing conditions) and SDS-PAGE were used ta separate the saline soluble muscle proteins. The results indicated that each population had a unique banding pattern. The similarity was high within each population. The dendrogram indicated that (Ml) and (M2) were much related to each other, while (Q) population was distantly related to the other investigated populations.