[Objective] In order to study control strategy of the Microcystis aeruginosa by native microorganism from Qingcaosha Reservoir water, the anti-Microcystis aeruginosa bacterium was isolated from Qingcaosha Reservoir water and its inhibitory effect on Microcystis aeruginosa was investigated. [Methods] Based on isolating and screening the bacteria cultured from the reservoir water, a strain CL capable of inhibiting Microcystis aerginosa was obtained. The inhibiting performance and influences parameters, such as culture time and concentration of bacterium on inhibitory effect were studied and 16S rDNA sequence analysis was done. [Results] Results showed that the inhibitory ratio would reach 45.4% when bacterium concentration ranged from 4.5×108 CFU/mL to 8.4×108 CFU/mL. Inhibitive effect first increased and then dropped with the culture time, the maximum inhibitory ratio appeared in the sixth day. 16S rDNA sequence analysis revealed that the strain CL belongs to stentrophomonas genus of xanthomonas family. [Conclusion] A native bacteria named stentrophomonas capable of inhibiting Microcystis aeruginosa was isolated from Qingcaosha Reservoir water, which has a certain potential use in controlling Microcystis aeruginosa of Qingcaosha Reservoir.