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This study aims to investigate and compare the biomarkers in the gingival crevicular fluid between the Han and Uygur subjects with healthy implants and peri-implantitis.Totally 80 subjects were divided into the H-case (Han patients with peri-implantitis), U-case (Uygur patients with peri-implantitis), H-control (Han subjects with healthy implants), and U-control (Uygur subjects with healthy implants) groups. Cytokine levels in the gingival crevicular fluid were detected, and the dominant bacteria species were analyzed.The matrix metalloproteinase (MMP)-13 level in the gingival crevicular fluid in the U-control group was significantly higher than the H-control group, whereas the C-reactive protein level in the H-control group was significantly higher than in the U-control group. No significant difference was observed in the dominant subgingival bacteria species between the H- and U-control groups. The levels of interleukin (IL)-1β and MMP-8 were significantly higher in the H-case group than the U-case group, whereas the IL-17A level in the U-case group was significantly higher. The shared dominant subgingival bacteria species of the case groups mainly included Prevotella, clostridium, Porphyromonas, treponema, Streptococcus, neisseria, and hemophilus. Moreover, Acinetobacter, Micrococcus, and Moraxella were found to be the specific dominant subgingival bacteria species for the U-case group. In addition, compared with the H-case group, the IL-1β levels were negatively correlated with Acinetobacter, Micrococcus, and Moraxella in the U-case group.Han and Uygur populations with healthy implants and peri-implantitis have differentially expressed cytokines in the gingival crevicular fluid. Moreover, dominant subgingival bacteria species differ between the Han and Uygur populations with peri-implantitis.