Abstract: There is limited information available on effects of aquaculture on lake ecosystems. Community structure and biodiversity of phytoplankton were investigated from July to September, 2015 in 23 lakes in the middle reach of the Yangtze River Basin, which include four groups: reservoir group (A), aquaculture ban group (B), low stocking aquaculture group (C) and high stocking aquaculture group (D). The analysis showed that dominant genera of the four groups were different. Group A was dominated by Pseudanabaena (Y=0.642) and Planktolyngbya (Y=0.064). Group B was dominated by Merismopedia (Y=0.428), Planktolyngbya (Y=0.118), Pseudanabaena (Y=0.133), and Scenedesmus (Y=0.066). Group C was dominated by Pseudanabaena (Y=0.395), Merismopedia (Y=0.097), and Planktolyngbya (Y=0.122). Group D was dominated by Merismopedia (Y=0.308), Microcystis (Y=0.118), and Pseudanabaena (Y=0.077). The phytoplankton abundance in group A was significantly lower than those in other lake groups (P<0.05). There was no significant difference in Shannon-Wiener index, Margalef index and Pielou index of phytoplankton among the four lake groups. The study indicated that fish culture could affect the abundance and dominant genera of phytoplankton, which may provide some implications for lake ecosystem management.