Colony formation plays an important role in the life history of Microcystis . However, analyzing the colony size distribution with a microscope is time consuming, and colony formation also hinders the direct monitoring of cell density. In this study, a quantitative protocol for rapidly analyzing the cell density and colony size distribution of pelagic and benthic Microcystis was developed. Microcystis colonies were disintegrated by alkaline hydrolysis with 0.01–0.05 mol L −1 sodium hydroxide at 85 °C for 6–8 min and automatically measured by the Flow Camera And Microscope (FlowCAM). Benthic Microcystis colonies were isolated from different lake sediments using 40 % Percoll solution. Alkaline hydrolysis was validated as a rapid and universally effective method to disintegrate different morphospecies of Microcystis colonies. The FlowCAM exhibited excellent accuracy, reproducibility, and efficiency in determining the cell density and size distribution of Microcystis . The developed protocol was successfully applied to field samples from Lake Caohai (China) and can accurately monitor the population dynamics and colony size distribution of bloom-forming Microcystis .