Fermented foods play an important role in the daily life and diet of the populations in Congo. Among these fermented foods, there is Pilipili or fermented pepper which is consumed without prior cooking. The microorganisms present are eaten alive. Few studies have been carried out on these microorganisms which may have beneficial effects on health. This study aimed to investing taxonomic diversity of bacterial communities in 3 samples of fermented peppers produced in 3 distinct areas of Brazzaville. To do this investigation, Illumina Miseq sequencing of 16S rRNA gene was used. The results showed that the number of identified operational taxonomic units (OTUs) ranged from 156 to 392. All OTUs belong to the domain of Bacteria and could be categorized into 21 Phyla, 36 Classes, 58 Orders, 100 Families and 171 genera. Firmicutes and Proteobacteria were the main dominant phyla of the total phyla present with a relative abundance of 89.12% and 8.08%, respectly. At the class level, Bacili were dominant in EB1 (99.50%), EB3 (85.32%) and EB2 (42.29%) while Clostridia in EB2 (40.10%). Lactobacillus, Clostridium sensu stricto and Frutobacillus were the dominant genera in the sample EB1, EB2 and EB3, respectively. The hierarchical classification showed that the samples EB1 and EB2 form the same group and EB3 is unique. Principal component analysis showed that the younger EB3 and EB2 samples were more diverse than the older EB1 sample. This study is a first in Congo on the diversity of fermented pepper using Illumina Miseq. It has shown that this food is very diverse and can be a source for the isolation of bacteria with biotechnological potential.