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The Random Amplified Polymorphic DNA (RAPD) was applied to analyze the genetic variation in three stocks of Labeo fimbriatus representing Cauvery, Vedavathi and Tungabhadra river streams of peninsular India. A total of 8 primers viz., OPA-07, OPP-11, OPB-17, OPF-01, OPF-03, OPF-12, OPD-19, OPP-16 were used to assay the polymorphisms among three stocks. The genetic relationships were studied based on polymorphisms generated by RAPD-PCR. The STATISTICA dendrogram based on the genetic distance matrix revealed a clear grouping of three stocks of fimbriatus into two clusters where in Cauvery and Vedavathi stocks together formed a cluster while Tungabhadra alone formed a separate cluster. It indicates that both Cauvery and Vedavathi are closely related whereas Tungabhadra was genetically away from other two stocks. The genetic distance within the stocks of Cauvery, Tungabhadra and Vedavathi stocks was 0.05, 0.12 and 0.11, respectively. It indicates that the Tungabhadra stock indicated higher proportion of heterozygous genotypes while Cauvery with more homogenate genotypes. Using this technique, only slight differences in genetic diversity were detected. Further, studying using mitochondrial DNA (mt-DNA) analysis, RFLP fingerprinting, or the sequencing of hyper variable regions of the mitochondrial genome may increase the validity of this conclusion.