Habitat segregation has been recognized as an important means of resource partitioning in river fish assemblages. Association between river fishes and habitat features were identified through principal component analysis (PCA). Fish and habitat data were collected in the Kaoping, Tsengwen, Choshui, and Tatu rivers from July 1997 to June 1999 in western Taiwan. Electrofishing was used to collect fishes in grids, and environment variables in the sampled areas were measured immediately after sampling. The first four PCs of depth, velocity, cover, substrate and water temperature variables explained 92.3% of the total variance in habitat characteristics. Varicorhinus barbatulus, Acrossocheilus formosanus and Tilapia mossambica in the upper right quadrant, indicated preference for deep-water habitat. Species usually associated with shallow water habitat include several minnow species. Rhinogobius brunneus, Hemimyzon formosanum, Sinogastromyzon puliensis and Crossostoma lacustre distribution is centred in the upper and lower left, indicating preference for shallow water. Principal component (PC) scores on Zacco pachycephalus, Abbottina brevirostris and Hemiculter leucisculus appeared to have no special preference. Differences in habitat use exhibited by these species may be related to success in finding food and avoiding predators.