Cyanobacterial bloom occured in Lake Gaoyang, Huangshi Dailizi and Shuangjiang Bridge of the backwater area of Xiaojiang River in Three Gorges Reservoir in late May of 2007. After the survey on the phytoplankton and water quality, it was found that cyanobacteria dominated the phytoplankton, taken up to the 81.43% of the total biomass, among which the Anabaena flos-aquaes was the dominance species. The heterocysts appearing in most species indicated that nitrogen fixation may occur. Low TN:TP ratio in April was that the heavy storm may trigger this nitrogen-fixation algal bloom. Phosphorus limitation was another characteristic, which is the result of the tremendous growth of phytoplankton. Lake Gaoyang may be the source place where algal bloom occured. Cyanobacteria moved downstream with the water flows, assembling at Huangshi Dailizi, where algal bloom was more than that in the Lake Gaoyang. As a result, total biomass and chlorophyll-a in Huangshi Dailizi was the highest among the sampling spots. Water velocity in Shuangjiang Bridge was slower due to the enlarged cross section downstream, offering a proper environment for the growth of cyanobacteria. Accompanied by the large amount of nutrients loads at Yunyang County, this may be the major reason of the detection of algal bloom in Shuangjiang Bridge.