Abstract: A fish-index of biotic integrity (FIBI) system, adapting to the middle and upper reaches of the Yangtze River and its attached lakes, was tentatively developed from the data obtained by the Yangtze Fish Resources Dynamic Monitoring Network, including the monitoring stations at Yibin, Banan, Wanzhou, Jingzhou,Yueyang, Hukou, the Dongting Lake and the Poyang Lake, from 2003 to 2008, by applying the principle of river health assessment, and on the basis of the system involving 12 indices proposed by Karr and modified by Fausch et al. In the process of development, the indices to be selected were listed in accordance with component characteristics of fish from the Yangtze and screened in combination with the results from the surveys of various indices. According to the Karr’s method, the authors don’t set expectation value and reference point respectively, instead of the differences among data from every monitoring station to value and score at three levels. The results showed that the fish biological integrity was “fair” in the upper and middle reaches of the Yangtze River, whereas in Dongting Lake and Poyang Lake the biological integrity both represented “poor”. Statistically, FIBI scores obtained by each monitoring station tended to decrease in six years.