The Deccan Mahseer, Tor khudree is an important food and game fish distributed in the up-stream mountain regions of the Deccan river systems and is popular in Indian Aquaculture due to its high food and aesthetic value. Since, the fish is listed as endangered in the IUCN Red List of Threatened Species, initiatives are essential for its culture and conservation. In the present study, 780bp of ATPase6/8 gene and 1kb of cyt b gene variations were used to analyze the population structure of the Deccan mahseer. A total of 152 samples collected from four riverine populations (TungaBhadra, Tunga, Periyar and Cauvery) were considered for the study. AMOVA revealed high among population variation of 50.83% with 10 haplotypes and within population variation of 49.17% in case of ATPase6/8 gene, but in case of cyt b gene, low among population variation of 14.87% with 21 haplotypes and high within population variation of 85.13% was seen. Pairwise FST analysis of ATPase6/8 gene indicated high genetic differentiation between Cauvery and Tunga population and no significant difference was seen between Cauvery and Periyar population. However, in case of cyt b gene pairwise FST analysis indicated high genetic differentiation between Cauvery and Periyar population and low significant difference was seen between Periyar and Bellary population. This study demonstrated high level of genetic structuring in the species.