Abstract: Based on the Illumina Miseq sequencing technology, the bacterial and fungal flora of the fresh Chaotian pepper (Capsicum annuum L.) and the line pepper (Capsicum frutescens L.) in Shandong and Shanxi province were sequenced during origin pre-processing. The diversity of bacterial and fungal community structure was analyzed, and the rationality and scientific of processing technology in different producing areas were also discussed. The results showed that the bacterial and fungal flora attached to the raw materials of the two red peppers were significantly different (P<0.05). After salting process, there were still significant differences in bacterial flora between the two kinds of pepper, while the differences in fungal flora gradually decreased with the progress of processing. According to the results of the count of cultivable microorganisms, the number of cultivable bacteria and fungi in the line pepper samples increased to 2.6×10⁶ and 1.6×10⁶ CFU/g after two-stage cleaning. However, in Chaotian pepper samples, the number of culturable bacteria and fungi after cleaning decreased to 9.0×10⁴ and 6.6×10³ CFU/g, respectively. It indicated that the same equipment was used to clean the line pepper with low applicability, resulting in the accumulation of microorganisms during the cleaning process. After salt mixing, the number of culturable bacteria and fungi decreased to 10²~10⁴ CFU/g. This study would reveal the community structure and diversity of microorganism during the primary processing of fresh red pepper, and provide a scientific basis for improving the processing level, the optimization of equipment, and quality control.