Abstract: In order to assess the ecosystem in the Hun River, F-IBI (fish-index of biotic integrity) was used to analyze data collected from 62 sites from May to June, 2010. Six indicators from 23 candidates were selected to establish the F-IBI system:total catches, percentage species of Leuciscus subfamily, Loach Fishes percentage, economic fish percentage, stain species percentage and widespread species percentage. F-IBI value of each indicator was calculated using the ratio method. Values below 75% were quartered to establish a health assessment as healthy, sub-healthy, fair, poor or very poor. The results showed that the percentages of healthy, sub-healthy, fair, poor and very poor sites were, respectively, 22.58%, 27.42%, 24.19%, 14.52% and 11.59%. The first three combined accounted for 74.19%. The poor and very poor sites were mainly distributed in the downstream of the Hun River. Pearson correlation analysis indicated that F-IBI was negatively correlated with electrical conductivity, but positively correlated with habitat quality. The results indicated that the upper reaches of the Hun River were at healthy, sub-healthy and fair levels, while the downstream areas were worrying, consisting of poor and very poor. These areas mainly suffered from impacts from the industrial zone of Shenyang City.