The present study is to understand the Bongseonsa stream in the National Arboretum fish fauna variation through comparison with historical data and to evaluate the stream health situated. We performed investigations over three times from April to September 2015. In the survey, 2,960 individuals which belonging to 22 species, 8 families were collected. Dominant species by number was Zacco platypus and subdominant species was Zacco koreanus. Seven Korean endemic species (Squalidus gracilis majimae, Microphysogobio yaluensis, Zacco koreanus, Koreocobitis rotundicausata, etc) were observed and showed a ratio of 36.4%. The community analysis revealed that the structure of fish community in the study sampling sites was instability in having dominance 0.79 (±0.15), diverse 1.21 (±0.60), evenness 0.58 (±0.15) and species richness 1.49 (±0.83). The values in the Qualitative Habitat Evaluation Index (QHEI) was averagely 122.9 (±44.8) in the Bongseonsa stream and this was showed to have favorable habitat surroundings. As a result of tolerance guild analysis, the total number of sensitive species and intermediate species were higher than tolerant species. Analysis was divided into A and B two groups of fiducial 12.25% in Cluster analysis degree of similarity between study sampling sites. Fish Assessment Index (FAI) was rated A and B grade in Bongseonsa stream that stream health showed favorable. However Wangsuk stream as a urban stream rated C grade and analysed the lowest grade in the whole study sampling sites. There was high correlation beteween FAI and various indexes, dominance, diverse, evenness and sensitive species and intermediate species.