One active fraction, which mainly contained many kinds of fatty acids, was extracted and isolated from the macrophyte Potamogeton malaianus, then was analyzed by the GC-MS. The EC_50,3d fraction on Selenactrum capricornutwn was 7. 90mg/L. The inhibition of eight fatty acids in the fraction and oleic acid on S. capricornutum confirmed that fatty acids had the al-lelopathic inhibitory effect and the effect was relevant to the carbon chain and unsaturated linkages,which meant the shorter the car-bon chain of the fatty acid, the stronger thegal growth inhibited, and the unsaturated linkages in the fatty acid,the stron-ger the algal growth was inhibited. The combined activity of multi-fatty acids showed synergistic growth inhibition on S. capricornu-tum. Mother fraction,which mainly consisted of sterols,was isolated from the extraction of P. malaianua,but it did not inhibit the growth of S. capricornutum and had no evident influence on the allelopathic inhibition of fatty acids on S. Capricornutum.