Colonial Microcystis aeruginosa were obtained when the unicellular algae were exposed to flagellate Ochromonas sp. filtrate. To investigate the benefit of this morphological change, flagellates were added into cultures of unicellular and colonial M. aeruginosa, respectively. The clearance rates of flagellates on algae were markedly decreased when they were cultivated with induced colonial M. aeruginosa. This result indicated that colony formation in M. aeruginosa was a predator-induced defense, which could reduce predation risk from flagellate. The increased content of soluble extracellular polysaccharide (sEPS) and bound extracellular polysaccharide (bEPS) may play an important role in adhering M. aeruginosa cells together to form colonies. The decrease of ΦPS II and the increase of sinking rates of induced colonial M. aeruginosa showed that the costs of grazed-induced colony formation in M. aeruginosa may reflect in the photosystem II efficiency, and in the sinking rates.