We assessed fish fauna and habitat suitability indexes in the Geum river basin. Field monitoring was conducted for ecological and habitat condition assessment at 23 sites from October 2007 to March 2009. The habitat suitability indexes established for dominant fish species using the monitoring data were employed to assess riverine health conditions such as composition ratio of fish species, richness and dominance indexes, bio-diversity(dominance index, diversity, evenness and richness), and water depth, velocity and substrate size. Twenty-one species(42%) including Rhodeus uyekii and Pseudopungtungia nigra were found endemic out of the 50 species in 11 families sampled during this study period. The most frequently found one was Zacco platypus(34.3%) followed by Z. koreanus(10.2%) and Coreoleuciscus splendidus(8.4%). For Z. platypus, the dominant fish species in the basin, the favored habitat conditions were estimated to be 0.1~0.9 m for water depth, 0~0.9m/s for flow velocity and silt(<0.1mm)~cobbles(100.0~300.0mm) for substrate size, respectively. Overall, it was concluded that the Geum river basin has been relatively well protected from the anthropogenic disturbance for the legally protected species including the endemic species studied in this study.