Evident effect of an algicidal bacterium Pseudomonas mendocina on the growth and antioxidant system of Aphanizomenon flos-aquae was detected in this experiment. Seven parameters including the chlorophyll a contents, Fv/Fm values, reactive oxygen species (ROS), malonaldehyde (MDA), catalase (CAT), peroxide dismutase (POD), and superoxide dismutase (SOD) were tested in the cyanobacterium A. flos-aquae cells after inoculation with the algicidal bacterium Pseudomonas mendocina DC10. It was shown from the experiment that the growth of the treated cyanobacterium A. flos-aquae was significantly restrained, which was expressed as great reductions in the chlorophyll a contents and Fv/Fm values. At the same time, the treated cyanobacterial cells exhibited an obvious increase in the production of ROS and MDA compared with the control. CAT and POD activities in the treated group kept at high level, however, they both reduced significantly on day 6. SOD activities in the treated A. flos-aquae showed obvious declines after inoculation, and great augmentations on day 3 and 4, thereafter, they kept in a declining tendency. The results showed the oxidative stresses induced by the bacterium could be a killing agent of the cyanobacterium A. flos-aquae cells.