Eutrophication of water due to pollution is one of the most serious environmental problems. The occurrence of toxic cyanobacterial blooms in eutrophic lakes, reservoirs, and recreational waters has become a worldwide problem. The inhibitory allelopathy of plants on harmful algae, which has drawn extensive attention recently, is low-cost and ecologically safe, and some good results have been reported. In this study, volatile organic compounds as major allelochemicals have been isolated from some aquatic plants and identified. The chemical compositions of essential oil isolated from Potamogeton cristatus, Potamogeton maackianus, Potamogeton lucens, Vallisneria spinulosa, Ceratophyllum demersum, and Hydrilla verticillata were analyzed by GC/MS. Thirty components were identified in the oils, mainly including fatty acids, ester, sterol, and ketone, etc. Inhibitory effects of essential oils on Microcystis aeruginosa were also investigated. The inhibition ratio of essential oils on M. aeruginosa was 30.2-41.7% when the treatment concentration of extracts was at a level of 50.0 mg/L. Hence, the essential oils isolated exhibited a significant anti-cyanobacterial activity.