Ecological information on the rivers of eastern Himalaya, specifically the state of Arunachal Pradesh is not studied well. The present study describes fish assemblage patterns and deriving relationships between local habitat variables in the upper reaches of Subansiri River, Arunachal Pradesh. This study was carried out during October to November 2014 and February to March 2015. A total of 26 fish species belonging to eight families were recorded, in which eight species are endemic to the eastern Himalayan region. Fish species richness varied from two to 18 species in the upper reaches of Subansiri River and high species diversity was recorded in Sigin Stream (H’=2.76). Based on the seven habitat variables (water velocity, depth, channel width, percentage of substrate composition, percentage of riparian vegetation, altitude, and water temperature) then streams were categorized into lower-order and higher-order streams using principal component analysis (PCA). The site-wise fish abundance data along with habitat variable information was then subjected to the canonical correspondence analysis (CCA) for testing the association of habitat variables on fish abundance. The CCA results revealed that the abundance of large-size barbs, Neolissochilus hexagonolepis, N. nigrovittatus, Schizothorax progastus, and S. richardsonii were strongly associated with high altitude, water velocity, rich dissolved oxygen, and good riparian vegetation. On the other hand, Channa gachua, Botia rostrata, Danio rerio, Devario aequipinnatus, and Garra nasuta showed strong association with warm water streams with more conductivity. Copyright:© Satpathy et al. 2021. Creative Commons Attribution 4.0 International License. JoTT allows unrestricted use, reproduction, and distribution of this article in any medium by providing adequate credit to the author(s) and the source of publication.