In this study, microbiota composition and cytokines were significantly different between healthy implants and peri-implantitis, and the genera of Peptostreptococcaceae XIG-1, Haemophilus, and Treponema, as well as cytokines such as IL-17A, IL-6, IL-15, and IL-1β, might facilitate the diagnosis of peri-implantitis. Here, IL1B is linked to Peri-Implantitis.