Abstract: In this study, Illumina MiSeq sequencing technology was used to analyze the bacterial community structure of Zha-Chili from Xingshan and Baojing. The α-diversity analysis showed that the community diversity and abundance of Zha-Chili in Xingshan were significantly lower than those in Baojing (P<0.05). Lactobacillus belonging to the Firmicutes was the main bacteria in the two places, the abundance of which was 50.24% in Xingshan and 88.26% in Baojing. β diversity analysis found that the bacterial community structure of Xingshan and Baojing Zha-Chili was significantly different on the whole (P<0.01) and 11 biomarkers were identified, among which Lactobacillus and Chishuiella were the most influential ones. Phenotypes prediction showed that bacterial groups of Zha-Chili of Xingshan were significantly expressed in movable elements, biofilm formation, gram negative, pathogenic potential and tolerance to oxidative stress, while the bacteria in Baojing Zha-Chili were significantly expressed in gram-positive.