The effects of an allelopathic fraction extracted from Phragmitis communis Trin on the growth of Selenastrum capricomutum and Chlamydomonas reinhardtii were investigated. Different amounts of the allelopathic fraction were added into the culture solutions in which the same amount of algae was inoculated in this study. During the cultivation, the algal density was determined by counting the number of algae under a microscope and the micro-structure of the algae was also observed. The results indicated that the allelopathic fraction showed significant inhibitory effects on the growth of S. capricomutum, and the value of EC_50.7d was 0.60mg/L. The algal cells of S. capricomutum in culture solutions with the allelopathic fraction enlarged obviously, and the microstructure was also greatly changed. The average width of cells of S. capricomutum in culture solutions with 6mg/L allelopathic fraction was one and a half times larger than that in the control group. No significant inhibition on the growth of C. reinhardtii was observed, but the motility of algal cells deciined after adding the aJlelopathic fraction.