Community structure of fish and inhabiting status of natural monument and endangered species, Cobitis choii were investigated in the Baekgok Stream, a tributary of the Geum River drainage system of Korea from May to November 2012. Ten-15 fish species inhabited upper stream (St. 1~St. 3) with a Aa or Aa-Bb river type composed of mostly pebble and cobble bottoms. 15~21 species did middle stream (St. 4~St. 5) with Aa or Aa-Bb type composed of mostly cobble, boulder and pebble bottoms. Nine species did Reservoir Baekgok (St. 6) with composed of mostly mud bottoms, and Seven species did Reservoir Baekgok outflow (St. 7) with Aa-Bb type composed of mostly boulder and cobble bottoms. And 20~23 species did lower stream (St. 8~St. 9) with a Bb-Bc type composed of mostly cobble and sand bottoms. A total of 35 species belonging to ten families were found in the stream during the survey. The dominant species were in the order of Zacco platypus (34.7%), Pungtungia herzi (9.4%) and Microphysogobio yaluensis (9.0%). Other abundant species included Tridentiger bifasciatus (8.2%), Pseudogobio esocinus (5.9%), Carassius auratus (4.6%), Squalidus chankaensis tsuchigae (3.7%), Rhinogobius brunneus (3.0%). Among residing species, ten (28.6%) species were endemic to Korea, one (Cobits choii) was endangered, and two (Micropterus salmoides and C. cuvieri) were non-indigenous. Natural monument and endangered species, C. choii were only inhabited St. 5, and they are inhabited 30~100 cm in water depth, sand bottom and slowly velocity. Using the mark-recapture method, populations were estimated at $7,838{pm}6,290$ individuals. Age group in May estimated from total length indicated that the 38~45 mm group is 0 year old, the 46~60 mm group is 1 years old, the 61~80 mm group is 2 years old, and the 81~93 mm group is more than 3 years old. Condition factor (${ imes}10^5) was 0.36~0.39 and 0.35~0.38 for female and male, respectively, and they are 13.5% were infected with parasites (digenea). We are discussed the health status, threats and conservation strategies of C. choii in the Baekgok Stream.