The volatile oils of two emergent plants (Typha latifolia and Arundo donax) were extracted with alcohol and then fractionated with some chemical reagent. Chemical composition of volatile oils were analyzed and identified by gas chromatograph-mass spectrometry (GC-MS). The volatiles appeared to form a complex mixture of 27 identified constituents, containing mainly fatty acids, ester, aldehyde, sterol, ketone, phenol, etc. Allelopathic activities of volatile oils on Microcystis aeruginosa were also determined. The results indicated that volatile oils from two emergent plants inhibited the growth of M. aeruginosa with inhibition rates of 43.3% and 47.9%, respectively, when the concentration of extracts was 50.0 mg/L.