Microcystis has become increasingly dominant during periods of algae bloom in freshwater environments where phosphorus (P) is usually the primary element limiting its propagation. In order to understand the mechanism of Microcystis dominance, the present study investigates the physiological, biochemical and ultrastructural responses of Microcystis aeruginosa (FACHB 469) to eight different inorganic phosphorus (Pi) concentrations under batch culture condition. The results showed that growth of M. aeruginosa was significantly restrained when Pi concentration was below 0.20 mg/L. Its alkaline phosphatase activity (APA) was induced under P deficiency stress and there was also a negative correlation between APA and external Pi concentration. Nevertheless, polyphosphate bodies (PP) were observed after M. aeruginosa, pre-cultured under Pi starvation, was exposed to higher Pi concentration. These results suggest that APA induction uptake and storage strategies of P might have ensured the dominance of M. aeruginosa in the freshwater environment with varying Pi concentrations.