The extracts of three emergent macrophytes (Acorus calamus, Oenanthe javanica, and Sagittaria sagittifolia) were tested to study their allelopathic activities on unicellular Microcystis aeruginosa, Anabaena flosaquae, Aphanizomenon flosaquae, and natural phytoplankton assemblages. The 72 h EC₅₀ of the most active extracts were measured. The results demonstrated the obvious species-specific activities of macrophytes on algae. Anabaena flosaquae and Aphanizomenon flosaquae was sensitive to the three macrophytes extracts, while unicellular M. aeruginosa was only sensitive to A. calamus and O. javanica extracts under the extracts concentration of 100 mg·L^-1. Only the extract of A. calamus roots showed high growth inhibition on the natural phytoplankton assemblages in Dianchi Lake (Microcystis water bloom). The 72 h EC₅₀ of A. calamus roots hexane extract on unicellular M. aeruginosa was 13.59 mg·L^-1, while that on natural phytoplankton assemblages was 48.75 mg·L^-1. These results demonstrated that the growth inhibitory activities of allelochemicals on unicellular M. aeruginosa cannot instead of the efficacies for controlling Microcystis bloom completely. And according to the different sensitivities of Microcystis species, the colonial Microcystis strains or natural Microcystis bloom will be proposed as the target organism when searching for Microcystis bloom control.