ObjectivesThis study aimed to investigate the relationship between microbial communities and the severity of peri‐implant mucosal bleeding in peri‐implant mucositis.Materials and MethodsSubmucosal plaque samples were collected from 54 implants divided into the healthy implant (HI) group, peri‐implant mucositis (PM) group, and peri‐implantitis (PI) group. Sequencing of 16S rRNA was performed using the Illumina MiSeq platform. Alpha diversity (i.e., Shannon and Chao index) and beta diversity were used to measure microbial diversity within and between microbial communities, respectively. Differences in microbial taxa between groups were assessed via linear discriminate analysis effect size. Correlation between the modified sulcus bleeding index (mSBI) and microbial dysbiosis index (MDI) was examined using Spearman correlation analysis and linear models.ResultsThe submucosal bacterial richness (Chao index) was positively correlated with the mean mSBI in the PM group. As the mean mSBI increased in the PM group, the beta diversity became closer to that of the PI group. In the PM group, the abundances of 47 genera were significantly correlated with the mean mSBI, and the MDI was positively associated with the mean mSBI. Fourteen of the forty‐seven genera were discriminative taxa between the HI and PI groups, and the abundances of these biomarkers became closer to those in the PI group in the progression of peri‐implant disease.ConclusionsA higher mSBI value corresponded to a higher risk of microbial dysbiosis in peri‐implant mucositis. The biomarkers identified may be useful for monitoring the progression of peri‐implant disease.