Morpho-genetic analysis in Bhagna, Labeo ariza populations was investigated to know the variation among them. Five different morphometric proportions were recorded and significant differences were observed (P<0.05). The genetic variations were analyzed in CA 6.1 buffer system. Among the 8 presumptive loci, the mean proportion of polymorphic loci were observed 25, 25 and 12.5% in the Atrai, the Jamuna and the Brahmaputra population respectively. The highest mean number of allele per locus was observed in the Atrai population (1.375). The mean proportion of heterozygous loci per individual was 4.305% for all populations. The results suggested that the considerable genetic variation is maintained among the natural L. ariza populations.