Proliferation of cyanobacteria is a global problem in eutrophic freshwater ecosystems. Silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis) have been considered effective in suppressing cyanobacterial blooms in eutrophic lakes. Long-term observations in Lake Donghu and Lake Qiandaohu documented that silver carp and bighead carp can efficiently suppress Microcystis blooms. However, the introduction of silver carp and bighead carp into blooming waters not always brings about the expected result, namely a decrease in phytoplankton biomass. Some ponds stocked with planktivorous carp have been reported to show an increase in phytoplankton biomass. One of the reasons may come from that the photosynthetic activity of Cyanobacteria after gut passage remains unaffected or even increases. In order to test the effect of silver carp and bighead carp's digest on Microcystis, chlorophyll fluorescence technique was employed. Chlorophyll fluorescence technique provides a swift, accurate, and nondestructive way for assessing the efficiency of photochemical conversion and it has become an increasingly powerful tool widely used in the study of photosynthesis. In our study, the growth and photosynthetic activity of Cyanobacteria after passage through the intestines of silver carp and bighead carp were compared with those taken directly from Lake Taihu during a 13-day in situ dialysis culture. The hypothesis for experiment reported in the study was that cyanobacteria in excretions might retain photosynthetic activity after gut passage. The aim of this work was to prove viability of the digested phytoplankton using multi-fluorescence parameters in comparison to the untreated water bloom from the same source population.Chlorophyll fluorescence parameters (including maximal optical quantum efficiency of PSⅡ(Fv/Fm), Potential activity of PSⅡ(Fv/Fo), effective optical quantu yield of PSⅡ(Yield), PSⅡ-driven electron transport rate (ETR), photochemical quenching (qP) and nonphotochemical quenching (NPQ)) were determined by PAM fluorimeter (Dual-PAM-100), and phytoplankton community structure and biomass were determined at the same time. The results indicated that Fv/Fm, Fv/Fo, Yield and ETR reduced significantly after passage through silver carp and bighead carp (P < 0.05), whereas qP and NPQ significantly increased (P < 0.05). After the first three to five days of reduced activity after excretion by silver carp and bighead carp, the metabolic activity of cyanobacteria recovered and rose significantly higher(P < 0.01) than the levels in the control population. The Fv/Fm, Fv/Fo, Yield and qP values were significantly higher in silver carp and bighead carp groups than in the control at the end of culture (P < 0.01), while NPQ was significantly lower on the 13^rd day (P < 0.01). The phytoplankton cell density and chlorophyll a content of silver carp group were growing faster than that of bighead carp group. The extrtracellular exopolysaccharide (EPS) of bighead carp group was higher than that of silver carp group during culture. At the end of the experiment, the total biomass of phytoplankton showed a 6-to 8-fold increase of growth in the two fish groups compared to the control. The relative biomass of green algae (Chlorophyta) and diatom (Bacillariophyta) increased a little, and their biomass was low when compared to cyanobacteria (93% of the total phytoplankton biomass). Moreover, EPS production was also stimulated after the passage through silver carp and bighead carp. The correlation analysis showed that the phytoplankton cell density, chlorophyll a and EPS concentrations in silver carp group showed significantly positive correlation with Fv/Fm, Fv/Fo, Yield, ETR and qP (P < 0.01), but significantly negative with NPQ (P < 0.01). In bighead carp group, the phytoplankton cell density, chlorophyll a and EPS concentrations were only significantly positive (P < 0.01) with ETR and significantly negative (P < 0.01) with NPQ. It was obviously that silver carp and bighead carp digestion do not cause fatal injury to Microcystis. And the Microcystis might exhibit over-compensatory growth resulting from fish digestion during cultivation. The increase in photosynthesis and growth of living cells after passage through the gut of silver carp and bighead carp may be one of the factors affecting the formation and maintenance of water blooms. Therefore, the use of silver carp and bighead carp as biological manipulation tool for cyanobacterial blooms control in lakes need more discussion.