Fluorescence excitation-emission matrix spectroscopy (EEMs) was applied to study the photobleaching of chromophoric dissolved organic matter (CDOM) in two surface water samples from Xiamen Bay exposed to natural sunlight between 10:00-16:00 during September 12-18, 2007. Both samples were collected from the lower and middle salinity areas in Jiulong Estuary of Xiamen Bay, and then filtered by 0.2 μm polycarbonate filters before the photobleaching incubation experiment. The results showed that three humic-like (C, A, M) and two protein-like (T, B) fluorescence peaks were observed in both samples, and the photobleaching didn’t cause obvious shift of the positions of these fluorescence peaks. The fluorescence intensities of the five peaks decreased with the increase in irradiation time and peak C demonstrated the fastest photobleaching rate. The photobleaching rate of low salinity sample was higher than that of middle salinity sample, consistent with its higher content of chromophores. All the five fluorophores could be distinguished into labile and refractory components based on their photobleaching dynamics. The increase in the intensity ratios of peak T and C (IT/IC) and peak T and C (IA/IC) after irradiation suggested that photobleaching can cause obvious change of the properties of dissolved organic matter in seawater, and it may partly account for the dominance of the protein-like fluorescence relative to the humic-like fluorescence in coastal area. The results suggest that EEMs was a useful tool to trace the transformation and removal processes of terrestrial CDOM entering the coastal regions.