Schizothorax esocinus is one of the important cold water delicious fish belonging to family Cyprinidae and found in River Swat which is one of the main river flowing in Khyber Pakhtunkhwa, Pakistan.The complete mitochondrial genomes of the S. esocinus species was found to be 16,591bp. Phylogenetic analysis of S. esocinus based on 12 s ribosomal RNA and 16S rRNA confirmed that, the phylogenetic position of S. esocinus was slightly different, but clustered closed to S. plagiostomus, S. labiatus, S. richardsonii, S. nepalensis, and S. progastus predicting a close homology in genome and hence a monophyletic line of evolution also this specie showed close relationship and homologs to the Aspiorhynchus laticeps, Spinibarbus sinensis, Aspiorhynchus laticeps, and Percocypris respectively. This study provided phylogenetic relationship between Schizothoracinae fishes and with the other fishes of family cyprinidae even at the subfamily level.
Keywords: Phylogenetics; S. esocinus; ribosomal RNA; river Swat.