This study investigated the difference in fish community structures in a main channel and an isolated former channel, considering the environmental factors in the Mangyeong River, Korea. Principal component analysis (PCA) with environmental factors showed that former channels were composed of a fine substrate covered by in-stream vegetation, whereas the main channel was covered by a wide range of substrates with a higher dissolved oxygen and conductivity. The result of the hierarchical cluster analysis with species abundance delineated to the four main groups; three abandoned channel groups and one main channel group. Non-metric multidimensional scaling (NMDS) showed that fish community structures of each study site differed from environmental factors: former channel fish communities were positively related to in-stream vegetation cover, whereas main channel fish communities were positively associated with dissolved oxygen and conductivity. The results indicated that channelization, where there was a separation between the former channel and the main channel, had detrimental effects on fish community structures of both the main channel and the abandoned channel in the Mangyeong River. In conclusion, this study suggested that the connectivity between the main channel and abandoned channel were required to enhance both habitat structural diversity and species diversity of the Mangyeong River.