Microcystis is a widely distributed genus of cyanobacteria that often forms surface blooms. The ability of Microcystis colonies to regulate buoyancy in response to variations in nutrients and light, and in the presence of low rates of turbulent mixing, is well described. Here, we report on the movement of individual cells within Microcystis wesenbergii colonies. Cells actively rearranged themselves within colonies, but randomly relative to other cells. Of the known types of cyanobacterial movement, gliding or twitching mediated by type IV pili was deemed the most likely causative mechanism. Transmission electron microscopy showed, however, no pilus-like structures on M. wesenbergii cell surfaces. We speculate that intra-colony movement may optimize colony fitness by helping individual cells to meet specific physiological requirements that may differ between the core and outer parts of the colony. This may increase fitness of cells and explain the recent dominance of M. wesenbergii in some New Zealand lakes.