This study is to investigate the subgingival bacterial diversity and community structure in the Uygur subjects with peri-implantitis.Totally 40 cases of gingival crevicular fluid were collected from Uygur subjects and divided into the Control group (healthy implants) and Case group (peri-implantitis), respectively. DNA was extracted, and the sequencing in the 16SrRNA V4-V5 region was conducted on the Illumina Miseq sequencing platform. The 16SrRNA gene clone library was constructed and analyzed.Totally 733,759 valid tags were obtained from these 40 samples. After comparing with the Silva-16S database by the Uparse software, 263 operational taxonomic unit were finally harvested (135 for the Control group and 128 for the Case group). The differential bacteria between these 2 groups at the phylum, class, order, family, and genus levels were Actinobacteria, Actinomycetes, Pasteurellales, Moraxellaceae, and Acinetobacter, respectively. The dominant genera with significantly different distribution between the Control and Case groups included Vibrio, Campylobacter, Granulicatella, Acinetobacter, Micrococcus, and Moraxella. The α diverstiy analysis based on the chao diversity index showed that there was significant difference in the microbiological diversity between these 2 groups. Principal coordinates analysis analysis indicated significant differences in the bacterial community structure between these 2 groups. Cluster analysis showed higher abundance of Micrococcus in the Case group, while higher abundance of Prevotella in the Control group.There are significant differences in the diversity of subgingival bacteria between the Uygur subjects with healthy implants and peri-implantitis. Moraxella, Micrococcus, and Acinetobacter might represent dominant bacteria genera causing peri-implantitis in the Uygur population.