The culture solution of M. spicatum was fractionated to three fractions; acidic, basic and water soluble fraction based on polarity. The assay of three fractions for blue-green algae (M. aeruganosa) showed that the water-soluble fraction was the only fraction that demonstrated inhibitory effects on growth of M. aeruginosa. Such result indicated that the water-soluble fraction contained allelopathic compounds secreted by M. spicatum. Thus, the water-soluble fraction was filtered through a membrane (molecular weight cut-off, MWCO 1000) in order to investigate molecular weight of the allelopathic compounds. A filtrate through the membrane did not affect the inhibitory effects of the water-soluble fraction. The water-soluble fraction filtered through the membrane was applied to an analytical high performance liquid chromatography (HPLC) system equipped with an electrochemical detector. Four polyphenolic compounds; ellagic (EA), gallic (GA), pyrogallic acids (PA) and (+) -catechin (CATECH) which were below MW 1000 were identified in the water-soluble fraction by the analytical HPLC system. These phenolic compounds showed inhibitory effects on the growth of M. aeruginosa. Among the four phenolic compounds, PA and GA were the most inhibitory to M. aeruginosa, while autoxidized PA and GA had the same inhibitory effects as PA and GA.