This study was carried on the Mahakali River from October 2007 to October 2008, which flows in western region of Kanchanpur district of Mahakali zone of Nepal. The purpose of this study to provide baseline information of the hill-stream fishes of Mahakali River and physiological modification. The sampling stations were established along the 10 km stretch of this river and dividing into two sections, each sampling station were 10km far from each other. Each sampling station was visited three times during the study period. A total of 16 times samples were collected with the help of cast net, scoop net and hook line. Altogether 44 fish species collected including 19 hill stream fish species recorded from the study site. This includes 5 orders, 12 families, 29 genus which represents the total collected species. Among them, 5 species were exotic and 39 species were collected from Mahakali river and irrigation canal along with other associated area. The family Cyprinidae found to be dominating species with 21 species, followed by family Cobitidae with 5 species, Bagridae represented by 2 species, Clariidae with 2 species, Channidae with 2 species, Mastacembelidae 2 species, Siluridae 1 species, Chandidae 1 species, Nandidae 1 species, Gobiidae 1 species and finally Anguillidae represent 1 species. Among them, altogether 19 species were hill-stream fishes. The hill-stream fishes like Labeo dero, Barilius barna, Barilius bendelisis, Barilius vagra, Raiamas bola, Brachydanio rerio, Esomus danrica, Garra annandalei, Garra gotyla, Tor Crossocheilus latius, Schizothorax plagiostomus, Schizothoraichthys progastus, Botia lohachata, Lepidocephalus guntea, Acanthocobatis botia, Schistura rupecula, Schistura corica and Glossogobius giuris were found.
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