AbstractIn India the distribution of genus Triplophysa has been reported only in the upper drainage of the Indus River in Jammu and Kashmir and Lahul and Spiti area of Himachal Pradesh. There is no study on the taxonomic characterization of this genus from Kashmir Himalaya. Therefore the present study was aimed to characterize two important fish species Triplophysa marmorata and T. kashmirensis from Kashmir valley, by using morphometric and molecular tools. It is difficult to discriminate these two species due to the poor quality of original descriptions, and the lack of good reviews. Keeping this in view, a morphometric and molecular study was conducted. Morphometric data were analyzed by using univariate analysis of variance (ANOvA) and multivariate analyses (Principal component analysis) and mtDNA marker Cytochrome oxidase 1 was used for molecular support. Altogether, 22 morphometric characters were used and 15 characters were found significantly variable (P < 0.05). First two components of principal component analysis (PCA) i.e. PC1 and PC2 grouped these two species into separate clusters. The Cytochrome oxidase 1 analysis showed that the mean intraspecific nucleotide divergence (K2P) was 0.001 and interspecific nucleotide divergence was 0.007. Despite having low K2P divergence, these two species got separated into two distinct clades in both Neighbour joining (NJ) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) tree building methods. But the pattern of clade formation showed that these species were recently radiated from each other and may have the same ancestor. Furthermore, these two species were found closer to Nemacheilidae than to Balitoridae family in the phylogenetic analysis. The molecular divergence between these species was also supported by variance in morphometric data. This work may build the base for the revision of taxonomic identity of these two important fishes of genus Triplophysa. The present investigation formulated that, based on morphological and mtDNA COI sequences analysis, these two taxonomic Triplophysa species should be considered as valid. The results may further assist to enhance the knowledge of the ichthyologists in understanding the ichthyofauna of Kashmir valley and will help them in planning strategies for conservation and management of these less studied small indigenous species along their natural range of distribution. Rev. Biol. Trop. 64 (2): 473-482. Epub 2016 June 01.