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Whole mitochondrial DNA (mtDNA) for Schizothorax esocinus sequence was found to be 16,591 bp with 13 protein-coding genes, 2 rRNAs genes, 22 tRNA genes, and 2 non-coding region. For estimating phylogenetic association of a species, protein coding genes of mitochondrial DNA are considered to be a great value. In this study, we sequenced protein-coding genes of Schizothorax esocinus, based upon which we compared the 23 Schizothoracinae fishes with S esocinus by phylogenetic association. We analyzed that S. esocinus to be closely associated with Schizothorax labiatus, Schizopyge niger, Schizothorax nepalensis with high-bootstrap values. Such empirical data would be important for understanding the phylogenetic relationship of Schizothorax species.