Genus Tor is an ecologically and economically important fresh water fishes under the family Cyprinidae. Taxonomy and phylogenetic relationship of this species are extremely confusing due to the morphological variation and habitat adaptation. Tor khudree and Tor mussullah was reported from River Chaliyar by earlier workers and presence of Tor malabaricus was confirmed through DNA barcoding. Tor samples were collected from the different localities of Chaliyar River, one of the west flowing rivers in Western Ghats. DNA barcoding using the mitochondrial COI (Cytochrome Oxidase Subunit 1) gene was carried out. Morphometric analysis was performed using twenty two morphometric and fifteen meristic characters. The existence of Tor khudree, Tor malabaricus and T. mussullah is confirmed through DNA barcoding and it enhance the fish biodiversity of river Chaliyar. Due to habitat change and indiscriminate fishing these species are under tremendous stress and it needs an urgent attention to conserve these threatened species