Abstract: By analyzing the changes of malondialdehyde（MDA）concentration，relative permeability
of cells and microstructure of red pepper tissues，the results indicated that the pulp tissues infected by
pathogens causing discoloration had significantly increased in MDA concentration，relative permeability
compared with control group（P < 0.05），as well as they destroyed cell membrane，tissue cells and
chromoplast structure，increased cell permeability，and decomposed pigment component. The bacteria
damaged the external and internal cell tissues，while the fungus damaged from the internal to external
tissues. The fungus had stronger damage to cell wall than bacteria，and were prone to destroy chromoplast
structure. Meanwhile，various pathogens damaged pepper tissues differently. Compared with Lysinibacillus
sphaericus and Cladosporium cladosporioides，the Bacillus subtilis，Phanerochaete sordida and Irpex
lacteus had more serious damage to cell wall，membrane and chromoplast structure，which decomposed
most inclusion and carotenoids，leaving a little lipid droplet. The experiment showed that the pathogens causing discoloration damaged red pepper cell microstructure，resulted in the damage of chromoplast，
decomposed pigment and consequently depigment.