In this study, we analyzed fish tolerance guilds in mainstems and tributaries of 65 streams and rivers arid their relations to water quality using dataset sampled from April to November, 2009. For the study, water quality parameters including biochemical oxygen demand (BOD), electric conductivity (EC), total nitrogen (TN), total phosphorus (TP), ammonia nitrogen ($NH_3$-N), nitrate nitrogen ($NO_3$-N) and phosphate phosphorus ($PO_4$-P) were analyzed in the laboratory and also tolerance ranges in 3 category fishes of sensitive, intermediate, and tolerant species with high abundance were analyzed. According to fish guild analysis, tolerant species was 58% of the total community and the proportion of omnivore species was 63% of the total, indicating a degradation of habitats and water quality. Water quality was shown typical longitudinal gradients from the headwater to the down-river; TN and TP increased toward the down-rivers except for the big point-source area and ionic contents, based on, electric conductivity showed same pattern. Tolerance guild analysis of 9 major species with high abundance indicated that sensitive groups had narrower tolerance range in the water quality than the groups of intermediate and tolerant species. In contrast, tolerant groups including Zacco platypus, Carassius auratus, and Opsarichthys uncirostris amurensis had wider tolerance ranges than the groups of sensitive and intermediate species. Thus, each group was evidently segregated from the tolerance levels. Principal Component Analysis (PCA) employed for the relations of water quality to fish species in each groups suggests that water quality had highest eigenvalues with fish species in the 1st axis of the PCA and nitrogen (TN, $NH_3$-N, $NO_3$-N) and phosphorus (TP) were key components differentiating three groups of sensitive, intermediate and tolerance guilds.