Background: The capture fishery sectors in the river and reservoir play an important role in the Indonesian economy through increased income and diversification of livelihoods. The present study was conducted to ascertain fish diversity and their distribution pattern in the upstream and downstream areas of Koto Panjang Reservoir, Riau Province-Indonesia. Methods: Fish samples were collected for a period of 12 months using a variety of fish nets at four sites; Koto Mesjid (KM) and Batu Bersurat (BB), located in the upstream area of Koto Panjang Reservoir and Rantau Berangin (RB) and Kuok (KK), located in the downstream area of Koto Panjang Reservoir. Data obtained were analyzed using standard taxonomic keys based on morphometric characters. Results: A total of 44 species belonging 19 families and 33 genera were recorded in the study area. Alpha diversity indices showed that fish diversity in this area was quite high (Shannon’s index = 2.10 and Simpson-D = 0.21) and evenness was low (evenness H/S =0.19). The fish in KM and BB sites (upstream) were from eight and 11 families, respectively. In RB and KK sites (downstream), fish were from 16 and 15 families, respectively. In KM, BB, RB and KK sites, the dominant family was Cyprinidae, comprising 33.45%, 50.95%, 43.04% and 39.35% of all fish caught at each site, respectively. Exotic species, especially Nile tilapia, were 20.15%, 14.11%, 5.62%, and 5.34%, respectively. Some differences were also noted between the upstream and downstream reservoirs, with a slight increase in exotic species in the upstream reservoir over the study period (from 11.39% vs. 34.66%), corresponding to decrease of native species (from 88.61% vs. 65.34%). Conclusions: The diversity and distribution of fish fauna were varied in upstream and downstream areas of Koto Panjang Reservoir. The exotic species were found to be dominant in the upstream reservoir areas.