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Background  The taxonomic validity of Northeast Indian endemic Mahseer species,  Tor progeneius  and  Neolissochilus hexastichus , has been argued repeatedly. This is mainly due to disagreements in recognizing the species based on morphological characters. Consequently, both the species have been concealed for many decades. DNA barcoding has become a promising and an independent technique for accurate species level identification. Therefore, utilization of such technique in association with the traditional morphotaxonomic description can resolve the species dilemma of this important group of sport fishes.    Methodology/Principal Findings  Altogether, 28 mahseer specimens including paratypes were studied from different locations in Northeast India, and 24 morphometric characters were measured invariably. The Principal Component Analysis with morphometric data revealed five distinct groups of sample that were taxonomically categorized into 4 species, viz.,  Tor putitora ,  T. progeneius ,  Neolissochilus hexagonolepis  and  N. hexastichus . Analysis with a dataset of 76 DNA barcode sequences of different mahseer species exhibited that the queries of  T. putitora  and  N. hexagonolepis  clustered cohesively with the respective conspecific database sequences maintaining 0.8% maximum K2P divergence. The closest congeneric divergence was 3 times higher than the mean conspecific divergence and was considered as barcode gap. The maximum divergence among the samples of  T. progeneius  and  T. putitora  was 0.8% that was much below the barcode gap, indicating them being synonymous. The query sequences of  N. hexastichus  invariably formed a discrete and a congeneric clade with the database sequences and maintained the interspecific divergence that supported its distinct species status. Notably,  N. hexastichus  was encountered in a single site and seemed to be under threat.    Conclusion  This study substantiated the identification of  N. hexastichus  to be a true species, and tentatively regarded  T. progeneius  to be a synonym of  T. putitora . It would guide the conservationists to initiate priority conservation of  N. hexastichus  and  T. putitora .

The Species Dilemma of Northeast Indian Mahseer (Actinopterygii: Cyprinidae): DNA Barcoding in Clarifying the Riddle