In the present study, we selected the common freshwater green alga Scenedesmus obliquus as the candidate cyanobacteria-control species by its allelopathic effect. The most common cyanobacterial species Microcystis aeruginosa was used as the target organism. The population growth of M. aeruginosa was inhibited by the green alga-conditioned media significantly. The influence was stronger when media concentrations increased from 0 to 100 %. In contrast, there was a strong and significant positive effect of the culture media from M. aeruginosa on the growth of green alga. Our results are useful and valuable as the experimental evidence for producing new cyanobacterial inhibitors and applying new environmental-friendly biological control methods in future. For one thing, we could use the green alga-condition media but not the green alga itself to inhibit the growth of M. aeruginosa. For another, although cyanobacteria are harmful for the environment, the condition media from cyanobacteria could also be viewed as the resource to stimulate the growth of S. obliquus, which is advantaged for gaining more green alga-condition media and food for fish.