A comparative study on seasonal variations of rotifer in different lake areas, including the riverine zone, Meiliang Bay, the central open water area and Gonghu Bay in Lake Taihu, was conducted from Jul. 2006 to Jun. 2007. Twenty-three rotifer species were identified in the riverine zone, 15 in Meiliang Bay, 14 in the central open water area and 21 in Gonghu Bay. The annual average density of rotifer was 475 individuals x L(-1) in the riverine zone, 164 individuals x L(-1) in Meiliang Bay, 189 individuals x L(-1) in the central open water area and 338 individuals x L(-1) in Gonghu Bay. The dominant species were different in the four different Lake areas.In the riverine zone, B. calyciflorus was the dominant species. In Meiliang Bay, B. angularis was the dominant species. However, in Gonghu Bay and the central open water area, P. trigla was the dominant species. The foods and suppression by large crustaceans are both important factors in determining the structure of rotifer community among the four differential lake areas in Lake Taihu. There were significant negatively correlations between the abundance of rotifer and the abundance of cladoceran, the biomass of cladoceran and copepod. The number of rotifers was positively related to Secchi transparency. Results indicate that the structure of rotifer community differs from the four differential lake areas in lake Taihu.