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Microcystis aeruginosa,as a dominant species of cyanobacteria,could arouse harmful algal blooms in freshwater worldwild.It has already seriously affected the human lives and prevented the use of water resource.There is hence an urgent to develop ecofriendly and effective methods to control and eliminate the M.aeruginosa cellsin the aquatic environment.In this paper,Halobaccillussp.strain H9,a bacterium that has ability to produce bioflocculant,was selected to assess its potential in removal of M.aeruginosa.The maximum flocculating rate could reach above 95% under appropriate condition with no addition of extra metal ions.The results showed that aggregation ofalgal cells was resulted from the flocculating active substance existed in strain H9 supernatant rather than direct contact by bacterial cells.The characteristics of supernatant with high thermal stability,pH stability and no damage to M.aeruginosacells make it great potential for use in regulation of harmful algal blooms.This is the first report on treatment ofM.aeruginosa pollution using the genus Halobacillus.