In lakes with seasonal cyanobacterial blooms, the pH fluctuates from slightly above 7 to around 10. In this study, we found that the abundance of gas vesicles in Microcystis species, in parallel to the buoyancy of cells, increased in response to elevation of the extracellular pH. Within 48 h after pH upshift, gas vesicle protein genes (gvp) were upregulated at both mRNA and protein levels due to reduced decay of gvp transcripts. The effect of pH on GvpC level was basically unaffected by inorganic carbon availability. This is the first report that long-term pH range plays a role in controlling gas vesicle formation in certain Microcystis species.