The fish community structure and inhabiting status of the endangered species Gobiobotia macrocephala and G. brevibarba were investigated at 10 stations in the Seom River, Korea from spring to autumn in 2010. During the survey, 37 species belonging to 10 families were found as inhabitants. A dominant species was Zacco platypus (36.2%), subdominant species were G. macrocephala (13.2%) and G. brevibarba (12.2%), and predominant species were Coreoleuciscus splendidus (8.1%) and Rhinogobius brunneus (4.9%). In addition, 18 species were endemic species to Korea; G. brevibarba and G. macrocephala were endangered species. The similarity index based on species composition and numbers clearly separated fish communities in the Seom River according to main sections, i.e., upper section (St. 1~3), middle section (St. 4~6) and lower section (St. 7~10). Dominance index gradually decreased toward the lower section, while diversity and species richness index gradually increased toward the downstream section. G. macrocephala resided in a fast-running downstream riffle with pebble and cobble substratum, while G. brevibarba inhabited the entire riffle with cobble substratum.