Poly-synchronous techniques were performed to investigate the inactivation and degradation mechanisms of Micro cystic aeruginosa under UV-C irradiation and chlorination. Extracellular dissolved organic matter (EDOM) and intracellular dissolved organic matter (IDOM) properties were analyzed using excitation emission matrix (EEM) fluorescence spectroscopy, while the concentration of biochemical parameters including protein, phycocyanin, chlorophyll-a, and microcystin-LR was determined. Transmission electron microscopy was also used to obtained ultrastructural images. EEM analysis revealed that protein-like matters were the major EDOM fluorescence component, while amino acid-like and protein-like matters constituted IDOM with little amount of humic-like substances. In addition, the monitor of biochemical parameters showed that they had different susceptibility under the inactivation reactions. Poly-synchronous techniques confirmed that UV-C irradiation was more appropriate than chlorination for M. aeruginosa inactivation and degradation. The primary mechanism of UV-C irradiation was direct photo-degradation and indirect oxidation by reactive oxygen species, which effectively degraded the fluorescence EDOM and IDOM and caused decomposition of cytoplasmic inclusions and intracellular bioorganic substances. Different from UV-C, the inactivation during chlorination was due to the formation of HOCI, which permeated into the cyanobacteria cells and caused intracellular damage, accompanied with incomplete degradation of IDOM and harmful MC-LR. Crown Copyright (C) 2011 Published by Elsevier B.V. All rights reserved.