Abstract: Cyanobacterial harmful algal blooms are a global environmental problem. Microcystis, which can produce microcystin, is one of the most pervasive bloom forming cyanobacteria in freshwater ecosystems. Blooms of Microcystis have adverse effects on lake ecology, and may effect human health, so it is important to control Microcystis blooms. In order to investigate the inhibitory effect of green algae on Microcystis aeruginosa based on allelopathy among different algae strains, we screened potential green algae to control M. aeruginosa blooms. One strain which has allelochemicals production properties was screened from 34 strains of green algae. The results showed that the spent medium of Scenedesmus sp. FACHB-1229 had the highest inhibition rate, for M. aeruginosa FACHB-3550 was 53.95% and for FACHB-905 was 48.85%, respectively. Result of gas chromatography mass spectrometry (GC-MS) indicated that 1,2-Benzenedicarboxylic acid, bis (2-methoxyethyl) ester might be the allelochemical substances. In addition, we also measured growth rates, high ammonia nitrogen tolerance and photosynthetic oxygen evolution rates of the strain. The results indicated that Scenedesmus sp. FACHB-1229 had high specific growth rate of (0.38±0.06)/d. It also had the highest photosynthetic oxygen evolution rates of (229.91±10.49) μmol O₂/(mg Chl.a·h). The ammonia nitrogen tolerance of Scenedesmus sp. FACHB-1229 was significantly higher than other strains, its growth rate was (0.30±0.08)/d when the ammonia nitrogen concentration reached up to 1888.60 mg/L. Moreover, the proportion of FACHB-1229 was consistently increased when co-cultured with FACHB-3550. In summary, FACHB-1229 has the superiority in interspecies competition with M. aeruginosa, its spent medium can inhibit the growth of M. aeruginosa, and it also has high ammonia nitrogen tolerance and photosynthetic oxygen evolution rate. Therefore, this study has provided the theory and application basis in prevention and control of cyanobacterial blooms using interspecific competition among algae. FACHB-1229 has the potential to control harmful algae through biological methods, it can grow rapidly in aquaculture pond or other polluted water bodies with high ammonia nitrogen concentration, while it can inhibit M. aeruginosa through allelopathy and provide dissolved oxygen at the same time.