Implants are exposed to a diverse oral environment and host responses that contribute to health or disease. For the last few decades, clinicians have relied on standard clinical and radiographic findings to assess the health of implants. However, recent studies involving the pathogenesis of peri-implantitis have identified microbial species and several putative biomarkers that could aid clinicians in this diagnostic process in the near future. This article provides an overview of the microbial species involved in implant health and disease and biomarkers found in oral fluids that relate to the underlying biological phases of a failing implant.