[Background] Cyanobacteria often form water bloom, seriously damage the aquatic environment and threaten aquatic organisms. Microbes can specifically inhibit the growth of cyanobacteria, and be used to control cyanobacteria bloom. [Objective] To isolate and screen bacterial strains with high algicidal ability against harmful algal bloom causing species—— Microcystis aeruginosa 7806, as well as the identification of the physiological, biochemical and molecular characteristics, meanwhile, algicidal mode and activity of the bacterium. [Methods] The physiology and biochemistry characteristics of strain hsn03 were studied by the API test kit. The 16S rRNA gene was sequenced and the phylogenetic tree was constructed. The algicidal activity was investigated by determination of the algicidal effect of bacterial cells, supernatant and bacterial culture on Microcystis aeruginosa 7806. The characteristics of algicidal substance were determined by measuring the algicidal activity of algicidal substance treated by different temperature, pH, protease K, organic solvent extraction, dialysis, as well as FTIR spectroscopy. [Results] Strain hsn03 possessed the highest similarity (99.59%) with the Bacillus sonorensis NBRC101234. Strain hsn03 showed high algicidal activity on M. aeruginosa through secreting extracellular algicidal substances, and the optimum addition amount of bacterial supernatant was 7.0% (v/v). The characteristics of algicidal substance was high thermal stability, pH stability and low molecular weight (500?1 000 Da), which was proved to be not protein and polysaccharide, and algicidal active compound was confirmed to contain triple bond and cumulated double bonds. [Conclusion] The excavation and identification of algicidal bacteria play an important role in enriching the resource of algicidal bacteria to control harmful algal bloom. By studying algicidal methods, effects and characteristics, we will lay the foundation for further application of algicidal bacteria to control Microcystis aeruginosa.