Capsicum chinense is a high pungency capsicum fruit specially produced in Hainan Province.A molecular biology method based on polymerase chain reaction(PCR) and denaturing gradient gel electrophoresis(DGGE) was developed to investigate bacterial community of Capsicum chinense,and the traditional isolation method was combined to acquire dominant microorganisms of Capsicum chinense.The results showed that Pseudomonas stutzeri,Lactobacillus plantarum,Lactobacillus brevis,which can be cultured,were screened in Capsicum chinense by traditional isolation method.The six bands'16S rDNA gene sequences were detected in Capsicum chinense by PCR-DGGE,among which Lactobacillus sp.was in a dominant position which is 65% of the total microorganisms.And Pseudomonas stutzeri is in a secondary position which is 16% of the total microorganisms.The browning and the softened coursed by microorganism is reported in Capsicum chinense for the first time.