Bio-control techniques, especially using ubiquitous algicidal bacteria, have the potential to remove harmful algae. Understanding the mechanisms with regard to the bacterial effect on algal cells will facilitate development of biotechnology processes. In the present study, Microcystis aeruginosa was exposed to the extracellular substances of Aeromonas sp. strain FM, a previously isolated cyanobacterial growth inhibitor. The aim of this study was to examine the physiological responses of M. aeruginosa to different amounts of the extracellular substances from Aeromonas sp. The results showed that the dehydrogenase activity and intracellular protein level were influenced by the dosage of the extracellular substances. The extracellular substances could enhance the release of extracellular polysaccharides of M. aeruginosa. During the treatment, superoxide dismutase activity and malondialdehyde content increased in cyanobacterial cells. On the other hand, a 1% and 3% dosage of the extracellular substances didn't cause the release of intracellular microcystins in short-time treatment (4 days). This study provides clues to understand the mechanism of indirect action of algicidal bacteria towards cyanobacterial cells.