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Instead of exploring variations in phytoplankton assemblages along one type of reservoir, this study identified similarities and differences in phytoplankton assemblages along two types of reservoirs. Phytoplankton assemblages from Xiaowan (storage reservoir) and Manwan (run-of-river reservoir) reservoirs in the Lancang River, China were used as case study. Taxonomic approach and functional group method were used to compare phytoplankton assemblages at sampling sites located in impounded areas of reservoirs, free-flowing areas directly below reservoirs, and free-flowing intermediate areas between the two contrasting reservoirs. With the reduction of reservoir disturbance, phytoplankton assemblages in free-flowing intermediate areas between reservoirs will recover to rich and diverse. Because of the inoculation and dispersion of phytoplankton from the upstream reservoir, dominant functional groups at the sampling sites located in impounded areas of reservoirs and free-flowing areas directly below reservoirs were mainly represented by groups that prefer long water residence times. The functional group TB (Nitzschia lorenziana) and W2 (Strombomonas ensifera) could be used as useful indicators to determine hydrological conditions due to their strong sensitivity to water residence times. Results of the linear redundancy analysis demonstrated that phytoplankton assemblages were mainly affected by DO and flow. 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