The effects of six emergent macrophytes (Typha orientalis, Acorus calamus, Oenanthe javanica, Scirpus validus, Sagittaria sagittifolia, and Pontederia cordata) on the growth of two strain Microcystis aeruginosa were studied under co-culture conditions. And the sensitivities of unicellular and colonial Microcystis strains to six emergent macrophytes were compared using an exudation experiment. Based on laboratory experiments, T. orientalis, A. calamus, O. javanica, S. validus, S. sagittifolia, and P. cordata had strong inhibitory effects on growth of unicellular M. aeruginosa, while only A. calamus and P. cordata show obvious growth inhibition on colonial M. aeruginosa. When the biomass density was 20 g FW·L^-1 growth inhibition rate of unicellular M. aeruginosa can exceed 90% for all of the six emergent macrophytes. When macrophytes coexisted with the colonial M. aeruginosa, only A. calamus, P. cordata, and S. sagittifolia showed the growth inhibition of algae. Maximal inhibition of Chl a growth was 75% (p<0.05) for A. calamus, 69% (p<0.05) for P. cordata, and 40% for S. sagittifolia at 45 g FW·L^-1 on day 15. The results of the exudation experiment indicated that there were no significant differences between control and treatment of Chl a concentrations of colonial M. aeruginosa for all of the six macrophyte exudations on days 6 and 12. While after 6 d incubation in 100% and 50% macrophyte exudations (40 g FW·L^-1), the cell densities of unicellular M. aeruginosa in control were obviously higher than all those in treatment (p < 0.05). The maximal algal growth inhibition (89.62%) of unicellular M. aeruginosa was achieved in 100% exudation of A. calamus on day 6 (p < 0.05). So according to the results of exudation experiments, the unicellular M. aeruginosa was more sensitive than the colonial strain to six emergent macrophytes. And this different sensitivity between Microcystis species probably correlated positively with colony size.