Dental implants represent the majority of treatment strategies used to replace missing teeth. However, peri-implant diseases caused by disturbance in peri-implant microbiological balance are among the reasons for implant failure. Since the 1980s, peri-implant microorganisms have been a hot research topic in dental microbiology. The bacterial ecology between the disease and health largely differs, which directly or indirectly increases the risk of peri-implant diseases. Accordingly, the determination of the 'core microbiome' of peri-implantitis and peri-implant mucositis is a key point of recent research.