Understanding habitat preference is an important consideration for the management of fish populations. We used multiple regression to describe relationships between environmental variables and catch-per-unit-effort (CPUE) of Sinogastromyzon puliensis (Homalopteridae). 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 fish in grids, and environmental variables in the sampled areas were measured immediately after sampling. Multiple regression showed that the most parsimonious model includes the linear effects of depth, velocity, and conductivity. The highest behavioral preference for depth occurred at 60 cm; it was similar between 20 and 40 cm and declined for very shallow and very deep water. S. puliensis preferred a wide range of velocities of between 0.8 and 2 m/s. Preference of substrate was highest for small rocks, and similar for pebbles and big rocks.