The aquatic biodiversity of Nepal is quite diverse, comprising around 186 indigenous and 11 exogenous fish species inhabiting various aquatic ecosystems such as freshwater rivers, streams, high altitude lakes and ponds etc. The 186 native fish species are distributed along the aquatic ecosystems of Nepal from lowlands of plain Terai to Mid-hilly terrains and the Himalayas with approximately 59 species categorized as cold water fish (Petr and Swar et al, 2002).

There is little knowledge about native fish species distribution and ecology, which is essential for ecological management and conservation biology of species. This requires the knowledge about species at population level that can sometimes be at low densities, which usually is based on visual detection and counting (Rees et al, 2014). However, unlike their terrestrial counterparts, relatively little is known about native fish and other aquatic life in Nepal.

Karnali river, which is the proposed site of the project, is among the 3 major river systems of Nepal. It is a perennial trans-boundary river originating on the Tibetan Plateau near Lake Mansarovar, with the extent of 507 km as being the longest river in Nepal, eventually joining the Ganges as one of its major tributaries (Jain et al, 2007). Due to the varying geographical features, large drainage area and volume of water, Karnali River is expected to provide diversified habitat for native and migratory fishes. There have been studies on aquatic biodiversity of Karnali river on morphological basis in the past, however molecular and genetic level study has not been performed until today (Smith et al, 1996). This research focusing on fish genetics and eDNA metabarcoding approach will help us to understand various strata of fish evolutionary history, biology and genetics in landscape level, thus aiding us to address issues of conservation biology or genetics of native fish biodiversity for the first time in Nepal.