Cladoceran, as one of the primary consumers in freshwater lake ecosystem, is sensitive to environmental change. So far, fruitful researches of subfossil cladocerans have been applied in many fields, such as paleoclimate reconstruction, food web, and nutritional changes and so on. However, most of studies focused on the lakes in boreal, temperate and subarctic zones, especially the alpine and deep lakes. Few works paid attention to freshwater shallow lakes in the middle and low latitudes of subtropics in Asia. Lake Taihu, located in the south of the Yangtze River Delta, is a large shallow lake covering over 2000 km² area which is also the third largest freshwater lake in China. Lake Taihu is ecologically divided into different basins. The west and north parts of Lake Taihu are observed increase of nutrient which has led to the emergence of non-N₂ fixing Microcystis sp. cyanobacterium causing serious cyanobacterial blooms and reduced biodiversity. The eastern part of Lake Taihu is also a mild eutrophic lake under the condition of growing large number of submerge plants. Those changes had influence on cladoceran composition and abundance. In this paper, we analysed the composition and abundance of cladoceran assemblages from cores and surface sediments and modern waters in spring, summer and autumn of the western, central and eastern parts of Lake Taihu. The results showed that Bosmina spp. was the dominant cladoceran of the sediments and water in different ecotypes of Lake Taihu. The composition of modern cladoceran was basically the largest number of cladoceran species in autumn. The cladoceran composition was single but with a high-level abundance in the western and central Lake Taihu. The cladoceran species in the eastern Lake Taihu were relatively rich but with a low-level abundance. The dominant species in the east part of Lake Taihu were composed of several species such as Bosmina spp., Chydorus sphaericus sl and Graptoleberis testudinaria. Over the past century, the composition and abundance of cladoceran in Lake Taihu had changed with the change of ecological environment. Especially, the change of the relative proportion of the eutrophic species (Bosmina longirostris) and the poor nutrient species (Bosmina longispina) indicated the evolution process of the eutrophication in Lake Taihu. At the end of 1970s, the western and central regions of Lake Taihu entered the eutrophication stage. The composition of cladoceran assemblages was single with a high-level abundance of Bosmina spp. and scarce littoral and benthic species compared with the eastern Lake Taihu. After 1960s, the cladoceran community in eastern Lake Taihu became relatively abundant but with a decrease of the abundance of cladocerans, which responded to the expansion of submerged vegetation biomass, swampiness and the aggravating eutrophication since 1960 AD.