The variation of the abundance of Cryptophytes was analyzed using monthly monitoring data during 2005 2009 in large shallow eutrophic Lake Taihu in China. The environmental factors and variations in cyanobacterial biomass were analyzed to explain the spatial and temporal distribution of Cryptophytes at three stations in Lake Taihu (Zhushan Bay, Meiliang Bay and Gonghu Bay). The results showed that:The mean biomass of the Cryptophytes in Zhushan Bay (1.89 mg/L) was much higher than that of Meiliang Bay (0.87 mg/L) and Gonghu Bay (0.43 mg/L); The average biomass of Cryptophytes in 2008 2009 (2.12 mg/L) was much higher than that in 2005 2007 (0.28 mg/L); Principally, Cryptophytes were most prevalent in Zhushan Bay which was marked by higher nutrient levels, higher organic matter and suspended solid concentrations. The succession of Cryptophytes was mainly affected by the grazing of zooplankton in Gonghu Bay. Furthermore, Cryptophytes and Cyanobacteria abundances were found to be inversely correlated, temporally, in Lake Taihu. Cyanobacteria seem able to reduce the biomass of Cryptophytes.