The river Sonkosh or Sankosh enters India at Jamduar (89°51/39.4// E and 26°43/59.8// N) of Kokrajhar district of Assam streaming from the snow fed upstream of Bhutan. It extends up to the Feshimari-Jaldhuaghat (89°47/26//E and 26°22/39// N) of West Bengal state. From the confluence point with another river called Raidak, It is known as Gangadhar river which flows through Dhubri district of Assam and joins with the Brahmaputra River. It has overlapping fishery resources of both warm and cold water nature, providing favourable conditions for many endemic fish species of Eastern Himalayan range. The spatial and temporal distribution of threatened freshwater fishes of Indian region that is enlisted by National Bureau of Fish Genetic Resources (NBFGR, 2010) was investigated at four sampling stations along the stretch of the river from April, 2014 to March, 2015. From the study, the conservation status of 11 fishes were recorded as endangered (EN) and 19 were vulnerable (VU) out of 30 numbers different fish species which are categorically in the status of threatened fresh water fishes of Indian region as described by NBFGR, Lucknow, India. Crossocheilus latius was recorded highest 10.62 % of relative abundances (RA) and less than 1% of RA was recorded for Channa barca, Ompok pabo, Sisor rhabdophorus, Tor tor, Bagarius bagarius, Ctenops nobilis, danio dangila, Eutropiichthys vacha and Ompok pabda. Their conservation status was also studied as comparison of CAMP, 98 and IUCN, 2014. We assessed diverse habitat characteristics in certain study sites of the river and are the natural breeding grounds of these threatened fish species. But due to installation Hydro-electrical power project in upstream of the river in Bhutan, the chance of changing its flow regimes, substrates, depth, sedimentation and any other unknown biophysical and biochemical alteration may leads to more threats to its endemic species. So the present information will serve as comparative hydro-biological assessment in future. It will also help in understanding the threat level and sustainability of threatened fishes. The river is important as it has the distribution of many endemic fish species of Eastern Himalayan region. So we recommend for protection and conservation of the Sankosh river and its fishery resources on priority basis. The study provides baseline scientific data which may be helpful in formulating new policies for conservation and sustainable development of lotic freshwater fishery resources of the region.