Allozyme electrophoresis was accomplished to identify genetic variation in two different strains of Nile tilapia, GIFU and GIFT. Two months aged experimental fishes were collected from two different regions namely Noakhali and BFRI, Mymensingh. Five enzymes namely LDH, SOD, MDH, ODH and MDH (NADP+) were used in TC-1 buffer system to analyze the genetic variation. LDH and SOD provided clear resolution for muscle tissue. Two presumptive loci were identified where Ldh-1* loci was found polymorphic in both populations. GIFT populations showed same mean proportion of polymorphic loci which was 50% whereas GIFU population showed highest mean number of alleles per locus which was 2.0. The highest mean number of effective alleles per locus was 1.47 and the mean proportion of heterozygous loci per individual was 24.31% which was found in GIFT population. Among two populations, observed heterozygosity (Ho) and expected heterozygosity (He) of GIFT population showed the highest values which was 0.333 and 0.254 respectively. The average observed heterozygosity (Ho) was 0.313 and expected heterozygosity (He) was 0.240 for GIFU populations. The average Ho/He value was 1.301 in Oreochromis niloticus population. The genetic differentiation (Fst) and the gene flow (Nm) over all two populations was 0.0239 and 10.1923, respectively. The genetic distance (D) between two populations was calculated and found to range from 0.0146 to 0.9855.