It is well recognized that gas vesicles influence the buoyancy of Microcystis and control the migration in the water column. Some of Microcystis strains do not have gas vesicles, so these strains cannot obtain buoyancy from them. In this study, we used two types of Microcystis strains such as the non-gas vesicle synthesizing strain M. aeruginosa UTEX-2061 and the gas vesicle synthesizing strain M. aeruginosa NIES-843 in the buoyancy control experiments of M. aeruginosa. By inducing colony formation and calculating the relative buoyancy rate of each strain, it was proven that the colony formation was strictly related to the buoyancy of both Microcystis strains. M. aeruginosa NIES-843 possessing gas vesicles could obtain buoyancy under the lower concentration of calcium and magnesium than M. aeruginosa UTEX-2061 possessing no gas vesicles. With the addition of the extracellular polysaccharides (EPS) extracted from Microcystis blooms into the culture medium, M. aeruginosa NIES-843 and UTEX-2061 could present higher buoyancy at the lowest concentrations of calcium and magnesium. It was suggested that EPS combined with the divalent metal cations such as calcium and magnesium made Microcystis form colony effectively. Calcium and magnesium ions enhanced the ability of colony formation of Microcystis and had a significant influence on buoyancy.