We examined the growth of testate amoebae preying on Microcystis whose physiological states were different in laboratory experiments and a hypertrophic pond. We prepared three experimental systems using water samples dominated by Microcystis aeruginosa: light incubation (control), dark incubation (dark), and light incubation with addition of nitrogen and phosphorus (?NP). In all the systems, the colony density of M. aeruginosa decreased slightly during incubation. Physiological activity of phytoplankton as determined by chlorophyll fluorescence was high and almost constant in the control and ?NP systems, whereas it decreased in the dark system. Cell densities of testate amoebae increased in the control and ?NP systems, whereas in the dark system they remained low. Thus, growth of the amoebae was low in the systems where physiological activity of Microcystis was low. In a hypertrophic pond, cell density of testate amoebae increased and remained high when M. aeruginosa predominated. Cell density of testate amoebae increased remarkably, simultaneously with the increases in M. aeruginosa colony density and phytoplankton physiological activity. We also found a significant correlation between densities of M. aeruginosa colonies and testate amoebae. We suggested that the physiological activity of Microcystis is one important factor affecting the growth of testate amoebae grazing on Microcystis.