Barbodes carnaticus is one of the important freshwater fish species widely found along the Cauvery river system of peninsular India. B. carnaticus belongs to the group of medium carps and attains large size. Information on the genetic makeup of stocks is extremely vital as it forms the basis for future genetic studies to improve captive breeding of the species. We used COI genes of mtDNA of B. carnaticus stocks collected from its natural habitat of Cauvery River system in Karnataka (Ramanathapura (30), Shivanasamudra (20), domesticated stock from CIFA, Hesaraghatta (22) and Tamil Nadu (Hogenakkal (24) and Chalakudy River in Kerala (Peringalkuthu (21). MtDNA analysis of B. carnaticus using COI gene shows that it has 12 haplotypes with an overall haplotype diversity of 0.451±0.062 and nucleotide diversity of 0.00097±0.00016. The data suggest that the Ramanathapura stock is having high diversity, while the Chalakudy stock is made of only one haplotype. The haplotype network revealed that there were differences in distributions and frequencies, and H1 was the most common and extensively distributed haplotype observed in the study. Each circle represents a haplotype and circle size is proportional to the haplotype frequency. The colors indicate locality according to the legend, and hatch marks represent the number of mutations by which haplotypes differ Fig 1. The observed unique haplotypes might be useful for differentiating the stocks. AMOVA analysis indicates that there is a significant genetic variation within the stock (89.74%), while between stocks the variation is around 10.26%. The genetic diversity studies help in identifying the similarities/ differences of the stock. Further, the study shows that it is important to form a base population from all the locations to conduct a breeding program of the species.