India is one of the mega biodiverse countries harbours the large number of endemic freshwater fishes in continental Asia. Among the freshwater fishes, the cyprinid fishes of the genera Tor, Parator, Folifer, Neolissochilus and Naziritor are often referred as mahseer and are endemic to continental Asia. Mahseer is famous as a game fish and is one of the favorite choices of the anglers across the world. Many of the mahseer fishes in India as well as in other Asian regions have been facing severe threats due to habitat loss, indiscriminate fishing etc. leading to reduction of population in the natural distribution areas. Of 32 mahseer species assessed under the IUCN criteria, 15 are listed as threatened under the "endangered" and "vulnerable" categories. Further due to taxonomic ambiguity, report on the available species of mahseers in India is highly species boundary and species delimitation. Molecular markers have been successfully used for studying evolutionary relationship between species. The present study is carried out to study the evolutionary relationship among selected mahseers using complete mitochondrial genome. Individuals of Tor putitora, Tor khudree, Tor tor, Tor mahanadicus and Tor malabaricus were collected from respective type locations. Complete mitochondrial genomes were amplified and sequenced by Iontorrent NGS platform. Less genetic divergence values were observed between T. putitora and T. mahanadicus. It indicates that T. mahanadicus could be a synonym of T. putitora and not a different species. The divergence value between T. malabaricus and T. khudree was significant (0.08) than within T. khudree species (0.02). Previously, T. khudree was synonymised as T. malabaricus. However, the present study results show that T. khudree and T. malabaricus could be two different species and cannot be synonymised with each other. In molecular phylogenetic analysis, T. mahanadicus clustered within a clade of T. putitora and confirms the synonimisation of these species. Tor malabaricus formed as a sister species to T. khudree species with significant bootstrap value (Fig.1)