A bacterium isolated from Lake Taihu was identified as Pseudomonas sp. A3CT, which performed different effects on Microcystis spp. Growth of Microcystis flos-aquae and Microcystis aeruginosa was assessed in co-culture with A3CT to determine the stimulatory or inhibitory effects on these toxic, bloom-forming Microcystis strains. Results demonstrated that the impacts of A3CT were species specific. A3CT promoted the growth of M. aeruginosa but inhibited growth of M. flos-aquae. To investigate the cause of this phenomenon, the chemical composition of A3CT exudates and the impact of exposure to A3CT exudates on the two Microcystis species were determined. Results suggested that the observed differential growth responses of the two microalgae to A3CT exposure might be related to two components in A3CT exudates NH4 (+) and cadaverine. Growth stimulation of M. aeruginosa by A3CT was significantly related to NH4 (+) concentration. Cadaverine possibly acted as a growth inhibitor of M. flos-aquae. The different effects of cadaverine on growth of the two Microcystis strains suggested that A3CT might play a role in intrageneric succession patterns observed during Microcystis blooms in Lake Taihu.