The invention discloses bacillus having an alga-lysing activity and application of the bacillus in controlling cyanobacterial bloom. The bacillus sp. Lzh-5 which has an obvious alga-lysing activity is separated from Lake Taihu water body, and has the preservation number of CGMCC (China General Microbiological Culture Collection Center) No. 8282; active alga-lysing ingredients, namely hexahydropyrrolo [1,2-alpha] pyrazine-1,4-dione and 3-isopropyl-hexahydropyrrolo [1,2-alpha] pyrazine-1,4-dione, are separated, purified and identified from a metabolic product of the bacillus, wherein median lethal doses LD50 of hexahydropyrrolo [1,2-alpha] pyrazine-1,4-dione and 3-isopropyl-hexahydropyrrolo [1,2-alpha] pyrazine-1,4-dione on microcystis aeruginosa 9110 are respectively 5.7mu g / mL and 19.4mu g / mL. The bacillus is applicable to research and production of novel biological algicides, and finally used for controlling cyanobacterial blooms of lakes.