Microcystis aeruginosa is one of the most common blue-green algae species that forms harmful water bloom, which frequently causes serious ecological pollution and poses a health hazard to animals and humans. To understand the progression of algal blooms and to provide a theoretical basis for predicting and preventing the occurrence of algal blooms and reducing the harm of algal bloom to environment, we investigated the diurnal variation of photosynthesis, ATP content and cell division in M. aeruginosa PCC7820. The results showed that the photosynthesis and ATP content of M. aeruginosa PCC7820 exhibited clear circadian rhythm with a period of approximately 24 h and that the periodic rhythms continued for at least three cycles under continuous light conditions. Furthermore, the period length showed that a temperature compensation effect and changes in light cycle or temperature could reset the phase of circadian rhythm. These results indicate that the circadian rhythms of physiological process in M. aeruginosa PCC7820 are controlled by the endogenous circadian clock. Examinations of the number, size and cytokinin content of cells also reveal that the cell division of M. aeruginosa PCC7820 with the generation time of 38.4 h exhibits robust circadian rhythms with a period close to 24 h. The circadian rhythms of cell division may be generated by a biological clock through regulation of the cell division phase of M. aeruginosa PCC7820 via a gating mechanism. The phases in which cell division slows or stop recur with a circadian periodicity of about 24 h.