Eutrophication has become a serious environmental pollution in aquatic ecosystem. The allelopathic potential of aquatic macrophytes against blue-green algae has received broad consideration. It has been reported that the growth of several submerged macrophytes could inhibit the growth of some deleterious alga, such as Microcystin aeruginosa, but many allelochemicals with antialgal effect are still unknown.This study compared inhibitory activity of volatile compounds from two submerged macrophytes, Ceratophyllum demersum and Vallisneria spiralis on M. aeruginosa. Essential oils of fresh and dry macrophytes were prepared using steam distillation procedure and extraction with diethyl ether. The components of the essential oils were analyzed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) and identified by standard retention indices, standard mass spectrum and co-chromatography with pure compounds. The relative amount of the each compound was calculated with peak areas integrator. The amount (in weight %) of essential oils was ten times more in the dry macrophytes than in the fresh macrophytes. When the essential oils were at a concentration of 100 mg/L, the fresh macrophytes had similar antialgal activities between C. demersum and V. spiralis while stronger than dry macrophytes. However, essential oils from dry macrophytes C. demersum showed stronger antialgal activity than V. spiralis. There exists a positive correlation between the concentration of the essential oils and the inhibitory activity. The EC50 (effective concentration for 50% inhibition of growth) was about 70 mg/L in the oil of dry C. demersum. The essential oils were composed of fatty compounds, terpenoids, phenolic compounds, phthalates, and some unknown compounds. The composition and relative amount of the essential oils were very different even though C. demersum and V. spiralis are two submerged macrophytes and usually coexist in aquatic environment. More than 40% of the total amount was phthalates in the essential oils of fresh macrophytes, but approximate 70% were fatty compounds and terpenoids in that of dry macrophytes. However, approximate 20% of the essential oils of fresh macrophytes were unknown compounds which were unstable and undetectable in dry macrophytes. Their chemical structures and bioactivities are in need of further study.