Peri-implantitis is a complex inflammatory disease affecting dental implants, characterized by microbial involvement, titanium particle release, and host inflammatory reactions. Conventional diagnostic approaches are limited, prompting exploration of biomarkers in saliva and peri-implant crevicular fluid. These include proinflammatory, anti-inflammatory, and bone metabolism-related markers. Advanced perspectives focus on gene polymorphism, proteomics, and single-cell RNA sequencing, which have illuminated detailed cellular interactions and inflammatory pathways unique to peri-implantitis. The future of peri-implantitis management trends toward precision medicine, leveraging genomic data and computational tools for personalized treatment strategies. A comprehensive understanding of peri-implantitis etiology and pathogenesis is crucial for developing effective targeted therapies to benefit patients long-term.