The present study investigates isolated extracellular polysaccharides (EPS) from algal blooms, and then concentrations of EPS and cationic ions in culture medium of disaggregated Microcystis aeruginosa were controlled by adding the EPS and cationic ions to make M. aeruginosa colonies under laboratory conditions. We examined the respective effects of Mg2+ ion, Ca2+ ion, and EPS on the colony formation, and subsequently the interaction of these factors was investigated to lower cationic ion concentration levels (i.e. < 1000 mg/L for Ca2+) in our previous study. The results showed that M. aeruginosa formed colonies in the Ca2+ + Mg2+ and the EPS + Ca2+ + Mg2+ media, and large colonies were found only in the EPS + Ca2+ + Mg2+ medium. Although M. aeruginosa required a high amount of Ca2+ ion (1000 mg/L) to form colonies in the previous study, the present work revealed that Mg2+ ion (250 mg/L) could decrease the Ca2+ ion concentration to 250 mg/L. Thermal analysis (TG/DTA analysis) of the EPS indicated that the EPS possessed surface functional groups such as carboxy groups. As the roles of cationic ions for the colony formation of M. aeruginosa, the present study suggests that Ca2+ ion contributes to the cross-linking reaction between negatively charged carboxy group on the EPS and M. aeruginosa cells, and Mg2+ ion acts as an agent capable of decreasing the Ca2+ ion concentration for the colony formation. It was also revealed that the EPS could induce the colony formation and expand the colony size of M. aeruginosa.