To investigate the nitrogen metabolism by M. aeruginosa and pH changes in the mediums under darkness, we cultured Microcystis aeruginosa, a dominant species in algal bloom, with different nitrogen forms including NO-3, NH+4, Bicine (N, N-Bis(2-hydroxyethyl) glycine) and Bicine + NO-3. Our results show that the densities of M. aeruginosa fluctuate within first 24 h of culture, and decrease after 24 h. However, the pH values in the mediums decrease significantly within the first 24 h in all experimental treatments and then gradually stabilize to a fixed value. The biggest decrease of pH value appears in the NO-3 medium, changing from 8.18 to 7.19. Interestingly, the biggest increase of NO-2 concentration appears in the same medium. The total amount of nitrogen decreases in all experimental mediums, specially in the medium containing Bicine and NO-3, and the decreased nitrogen is transformed to N2 through denitrification, then escaping from water into air. The results suggest that denitrification of M. aeruginosa happens when nitrate is supplied under darkness.