The objectives of this research were to analyse the microhabitat of Cobitis choii which is designated as an endangered fish species (I) and national monument species in Korea (No. 454), and provide valuable information of suitable replacement habitat in the future for a conservation of the population with rapid decreases by environmental pollution. Sampling and microhabitat analysis in three streams such as Baekgok, Yugu and Gap Stream, known as one of the least habitats in Korea showed that the mean number of Cobitis choii observed was 2.6. This result indicated that the richness was too low, so the species conservation was very urgent. Optimal physical microhabitat of the population was determined as environmental conditions with > 60% sand with 1 mm particle size, optimal water depth of 20 - 60 cm in the habitats, and the optimal current velocity of < 0.4 m/s. Under the circumstances of the microhabitat, optimal water volume (discharge) was 0 - 2 m3/s in the each sectional analysis and this reach was mainly composed of the stream section with intermittant slow runs and pools. These microhabitats were largely disturbed by physical modifications of habitat and chemical pollutions due to direct influences of nutrient-rich water inputs from the urban area and intensive agricultural pollutants. For these reasons, optimal habitat replacement are required in the future for the conservation of the species.