This narrative review examines the microbial profiles of healthy peri-implant sites, peri-implant mucositis, and peri-implantitis, along with the associated microbiological sampling and analyses. Healthy peri-implant sites are characterized by a stable community dominated by *Streptococcus*, *Rothia*, *Neisseria*, and *Corynebacterium* species, which prevent pathogenic colonization. Peri-implant mucositis shows increased microbial diversity, including both health-associated and pathogenic bacteria, contributing to early tissue inflammation. Peri-implantitis is marked by even greater microbial diversity and a complex pathogenic biofilm, with predominant pathogens such as *Porphyromonas gingivalis*, *Tannerella forsythia*, *Treponema denticola*, and *Fusobacterium nucleatum*. Other less common species like *Staphylococcus* and *Enterobacteriaceae* contribute to disease progression through biofilm formation and increased inflammatory response. The review also highlights the role of *EBV* and human cytomegalovirus in disease progression and the involvement of *Candida albicans* in biofilm formation and immune modulation. Advanced microbiological techniques, such as next-generation sequencing (NGS), have provided new insights into the microbial communities associated with peri-implant diseases, emphasizing the need for standardized diagnostic criteria, advanced molecular techniques, and integrated microbial data with clinical factors.This narrative review examines the microbial profiles of healthy peri-implant sites, peri-implant mucositis, and peri-implantitis, along with the associated microbiological sampling and analyses. Healthy peri-implant sites are characterized by a stable community dominated by *Streptococcus*, *Rothia*, *Neisseria*, and *Corynebacterium* species, which prevent pathogenic colonization. Peri-implant mucositis shows increased microbial diversity, including both health-associated and pathogenic bacteria, contributing to early tissue inflammation. Peri-implantitis is marked by even greater microbial diversity and a complex pathogenic biofilm, with predominant pathogens such as *Porphyromonas gingivalis*, *Tannerella forsythia*, *Treponema denticola*, and *Fusobacterium nucleatum*. Other less common species like *Staphylococcus* and *Enterobacteriaceae* contribute to disease progression through biofilm formation and increased inflammatory response. The review also highlights the role of *EBV* and human cytomegalovirus in disease progression and the involvement of *Candida albicans* in biofilm formation and immune modulation. Advanced microbiological techniques, such as next-generation sequencing (NGS), have provided new insights into the microbial communities associated with peri-implant diseases, emphasizing the need for standardized diagnostic criteria, advanced molecular techniques, and integrated microbial data with clinical factors.