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 A degrees 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.