Lake Taihu is subject to severe eutrophication due to high nutrient inputs. We compared the macrozoobenthic assemblages of Lake Taihu in 1987À1988 and in 2007 Changes in benthic communities between the two periods were significantly different among the four lake regions (the River Mouth, the North Bay, the Open Lake, and the East Bay), corresponding well with the changed environmental conditions. The River Mouth and North Bay showed the greatest changes in benthic fauna, corresponding with severe degradation in water quality. In 1987À1988, benthic communities were dominated by Tubificidae and Bivalvia in the River Mouth and the North Bay, respectively. In 2007, however, benthic fauna were mainly dominated by Tubificidae in the North Bay and total macrozoobenthos increased approximately 18-fold in abundance. The Open Lake was dominated by bivalves (mainly Corbicula fluminea) in both sampling periods, whereas an increased abundance of bivalve was observed from 1987À1988 to 2007. In the East Bay, which was covered by abundant macrophytes, the macrozoobenthos community decreased in abundance and was characterized by high species richness of gastropods. In addition, the abundance of gastropods, tubificids, and chironomids increased significantly between the two sampling periods. The relatively stable ecological conditions in the East Bay (e.g., trophic state and spatial distribution of macrophytes within the East Bay) might be responsible for the relatively small changes. Our results showed complex variation patterns of macrozoobenthic assemblages among different sections of Lake Taihu, which may be associated with the great environmental heterogeneity in this large shallow lake.