We found that most of subunits in crude Photosystem II particles (crude PSII) from a marine centric diatom, Chaetoceros gracilis, were degraded during incubation for 18 h at 25 °C in the dark (Nagao et al., 2010). In this study, we attempted to suppress the protein degradation by addition of protease inhibitors to the crude PSII during incubation for various times at 25 °C in the dark. When no proteases inhibitor added to the crude PSII, fucoxanthin chlorophyll a/c-binding protein (FCP), especially upper subunits of FCP, were first degraded, followed by most of PSII subunits. The degradation was slightly suppressed by a metal protease inhibitor, EDTA, or a serine protease inhibitor, PMSF, and the proteolysis activity of metal protease is slightly stronger than that of serine protease. On the other hand, the significant suppression was observed only by both EDTA and PMSF. These results suggest that the metal and serine proteases are associated with the crude PSII and the primary target of the proteases is the upper subunits of FCP.