Seasonal dynamics of phytoplankton biomass and microcystins content, and the selectivity of phytoplankton by two freshwater bivalve mussels (Hyriopsis cumingii and Cristaria plicata) were investigated from November 2004 to October 2005 in two bays of Lake Taihu with different nutrient status. We also studied the ecological effects of silver and bighead carp on phytoplankton. During the survey period, 71 phytoplankton genera were identified belonging to eight phyla: Cyanaphyta, Chlorophyta, Bacillariophyta, Cryptophyta, Euglenophyta, Pyrrophyta, Chrysophyta and Xanthophyta. Cyanaphyta and Chlorophyta comprised over 90% of total numeric abundance. Dominant phytoplankton were Chlorophyta during May and July, and Cyanaphyta in the other months. There were significant differences in both biomass and structure of phytoplankton between the two bays. Biomass of phytoplankton was significantly higher in Meiliang Bay (0.56-10.31 mg/l) than in Gonghu Bay (1.02-7.31mg/l) (p < 0.05, n = 36). Microcystis was an absolutely dominant spicies, significantly correlated with N loading. It appeared in May, increased dramatically in June, and peaked (3.7×108 cells/l) in July. There were also significant differences in both density and biomass of Microcystis between the two bays (p < 0.05, n = 36). The toxins from phytoplankton samples were identified as microcystin (MC), including three variants, MC-LR, MC-RR and MC-YR. The intracellular MC content, ranging from undetectable to 5.80µg/l, was relatively high in summer (from July to September) when heavy cyanobacterial blooms occurred. The highest amounts of intracellular MCs were found in the July samples from Gonghu Bay. The mean concentration of intracellular MCs was much higher in Gonghu Bay than in Meiliang bay (p<0.01). The intracellular MC content was positively correlated with Microcystis biomass in both bays. The reason for the lower MC concentration in Meiliang Bay whereas Microcystis biomass was higher might be due to a lower ratio of toxic to nontoxic strains. Percentage of Microcystis in total phytoplankton in the gut contents of two mussels (Hyriopsis cumingi and Cristaria plicata) were much lower than those in water column, indicating that both mussels had an ability of rejecting Microcystis. The selectivity of Microcystis by mussels declined with increasing percentage of Microcystis in the water column. Both mussels preferred Scenedesmus, probably because Chlorophyta are a good food. This favor of mussels was little influenced by Microcystis but strongly suppressed by Ulothrix. Because of intense feeding of silver and bighead carp on phytoplankton, Microcystis biomass was much lower in the fish pens than in the surrounding lake waters. Grazing pressure of silver and bighead carp not noly decreased total phytoplankton biomass and microcystin concentration, but also changed structure of phytoplankton community. These indicate that it is an effective way to control the Microcystis blomms and microcystins product through non-traditional biomanipulation.