The study was conducted in 2007~2008 in order to understand preference of physical microhabitat on the $1^{st}$-class endangered species, Gobiobotia naktongensis inhabiting the Gam Stream, tributary of Nakdong River. The total number of fish caught from the study sites was 3,671 representing 7 families 24 species. There were 8 Korean endemic species including Odontobutis platycephala, and 2 introduced species (Carassius cuvieri, Micropterus salmoides) were found. According to investigation and analysis of physical microhabitat on Gobiobotia naktongensis caught in the Gam Stream, a total of 57 individuals were found at shallow depth (0.14~0.46 m) and run (0.239~0.585m $sec^{-1}$). As a result of sieve analysis, stream beds consisted of about 1% gravel and 99% sand (83.4% coarse sand, 15.6% find sand). Therefore, Gobiobotia naktongensis seemed to inhabit shallow-run with coarse sand bed than deep-pool microhabitat. The findings indicate preference of physical microhabitat on Gobiobotia naktongensis, and it is important to enhance efficiency of fish conservation and ecological restoration with understanding species-specific characteristics in microhabitat including protected species.