In laboratory culture Microcystis aeruginosa occurs mainly as single cells but under natural conditions, it is normally in the colonial morph. This phenomenon suggests that some factors may be responsible for the occurrence of colonies in lakes. In the present experiment we investigated the grazing effect of flagellate Ochromonas sp. on physiological changes in M. aeruginosa using flow cytometry. The experiment was run in triplicate for 9 days at 25℃ in photoperiod of 12L:12D. Results showed that M. aeruginosa population exposed to flagellate grazing decreased sharply and some single cells formed colonies, most of which were made up of several or dozens of cells. Colony formation can deter flagellate from further grazing on a certain extent. Esterase activity and chlorophyll fluorescence of M. aeruginosa cells under flagellate grazing were significantly higher than those of unicells in the control, whereas the cell size of M. aeruginosa became smaller under intense flagellate grazing. The enhanced esterase activity may contribute to colony formation. The fact that cell size of M. aeruginosa under flagellate grazing became smaller may indicate that M. aeruginosa adopt a kind of ecological strategy to grow rapidly under intensive grazing.