Peri-implant diseases (peri-implantitis and peri-implant mucositis) are bacterially driven infections. Peri-implantitis leads to aggressive bone resorption and eventual loss of the implant. Traditionally, peri-implantitis was regarded as microbially similar to periodontitis, and translocation of periodontal pathogens into the peri-implant crevice was considered as a critical factor in disease causation. However, evidence is emerging to suggest that the peri-implant and periodontal ecosystems differ in many important ways. The purpose of this review is to examine the evidence supporting microbial congruence and discordance in these two communities. Current evidence suggests that osseointegrated implants truly create unique microenvironments that force microbial adaptation and selection. Further studies that revisit the "microbial reservoir" hypothesis and identify species that play an etiologic role in peri-implant disease and examine their transmission from teeth are needed.