The fish community of small freshwater ecosystems gets easily disturbed by direct or indirect human induced disturbances during the period of urbanization. Urbanization is one of factors that generate changes in stream and influences fish fauna in developed countries. This study was conducted in Busan Metropolitan City from 2001 to 2004. In order to investigate the fish community, the city was divided into 3 parts, eastern, central and western. A total of 3,206 individuals of 46 species from 19 families were collected from 55 sites. The dominant species was Rhynchocypris oxycephalus, whereas Zacco temminckii was the subdominant species. Cluster analysis was conducted using primary freshwater fish species collected from each stream. As a result of the analysis, study sites were well differentiated into 3 parts. Two species of Z. temminckii and R. oxycephalus represented the upper part of the stream and Carassius cuvieri, Acheilognathus rhombeus, Hemiculter eigenmanni and Micropterus salmoides represented the middle and lower parts of the stream. When compared with previous studies, fish community of the eastern part of the Busan city where urbanization is in progress, showed similar patterns to the central part. At the time of the habitat restoration of fish fauna in stream, appropriate selection of fish species should be made through analysis of stream character and biogeographic distribution of fish, and long-term monitoring is also needed for sustaining the management of fish fauna.