This study is focused on the antimicrobial activity of cyanobacteria Microcystis aeruginosa by the reduction and oxidation reaction of copper and zinc alloy metal fiber filter. Cu/Zn ion is easily makes radicals with molecular hydroperoxide. Especially, hydroperoxide radical shows strong toxicity to the strains. Plasma membrane causes conformational change when hydroperoxide radical binds to plasma membrane. Elution of copper ion from copper and zinc alloy metal fiber is detected in the cyanobacteria solution as 0.5 ppm, and that of zinc ion is 0 ppm respectively. Zinc ion is figured to form a hydroxide in the cyanobacteria solution and precipitated to form a sludge. The concentration of chlorophyll-a in the cyanobacteria solution was proved to be the index of antimicrobial level of Microcystis aeruginosa.