Information on trophic ecology can provide an understanding of the functional role of fish in an ecosystem, including endemic and native fish groups, as well as alien fish that are introduced through anthropogenic activities. The research on the trophic ecology of the fish community in the Nimbai Stream, Prafi River system, is intended to describe the interaction of competition and predation, especially towards endemic fish, Melanotaenia arfakensis. Fish samples were collected monthly from four habitat types, i.e., slow littoral, medium littoral, pool, and run from May 2016 to April 2017. A combination of an electric shocker and a hand net was used to collect fish samples. A total of 16 fish species were collected, consists of one endemic species, namely M. arfakensis, nine species of native fish, and six species of alien fish. The Arfak rainbowfish and three native fish species were categorized as insectivorous, four native fish species as herbivorous, and two other fishes as carnivorous. Three alien fish species also belong to insectivorous, two alien fish species as carnivorous, and one species as herbivorous. The niche breadth of fish communities ranges from 0.071 to 0.857. The trophic niche overlap between the Arfak rainbowfish and three native fish species and three alien fish species was recorded. The results of this study indicate a potential competition and predation interactions between Arfak rainbowfish and native fish as well as with alien fish species. Therefore, introducing alien fish into Prafi River system will disrupt Arfak rainbowfish population.