Aquatic ecosystems can harbour more than one non-native fish species and this can represent a threat due to trophic interactions with native fishes. However, research on interactions amongst multiple co-occurring native and non-native fish remains scarce. In this study, 551 organisms from 44 native fish, 11 non-native fish, 35 macroinvertebrates (of which one was non-native), together with 162 samples of basal resources were collected from six rivers of the Lower Pearl River Basin of China. Nitrogen and carbon stable isotope analysis was used to calculate community-wide trophic metrics and the degree of trophic overlap between native and non-native fish at both the community and functional feeding group level, together with diet composition. At the community level, there was a high degree of trophic niche overlap between native and non-native fish as a result of similarities in trophic characteristics. At the functional feeding group level, both native and non-native functional feeding groups demonstrated the capacity to occupy the niche space of each other. A significant trophic niche overlap, exceeding 50%, was found between non-native detritivorous and omnivorous fish, suggesting competition. The difference in diet composition between some native and non-native fish depended on the category of diet source across the rivers, suggesting dietary segregation. Albeit limited, the present findings suggest that trophic interaction between native and non-native fish is likely to reach a dynamic equilibrium status in the community owing to trophic segregation of fish species and the antagonistic effects amongst non-native fish.