Large amounts of sewage with nitrogen, phosphorus, potassium and other nutrients into the river lake will cause the algae bloom. Algae-lysing bacteria which can effectively degrade cyanobacteria in water is a potential treatment. An algicidal bacterium against toxic Microcystis aeruginosastrain G6 is isolated from reed roots in Baidu port of Taihu Lake. According to phylogenetic analysis, strain G6(Bacillus sp) is identified as Bacillus sp.The strain G6 which cultivated to the logarithmic phase is voted to water with bacteria and algae ratio of 1:10. The Chl-a of algae fluid could be reduced up to 82% when it is placed in the light incubator of 28℃ temperature, light intensity 2 500 lux, and photoperiod 12 h:12 h for 7 days. Strain G6 has the character that it can kill the algae cells without light. It is conducive to bacteria breeding and degradate algae in the deep sea which lack of light. The strain G6 could produce substance which can dissolv algae to kill microcystis aeruginosa, which is an indirect way to kill algae. The substance has thermal stability to kill the algae cells at high temperature.