Introduction: Although many studies have evaluated microbial composition of peri-implant pockets, the role of mycobiome on peri-implantitis is not well established. Objectives: The aim of this study is to characterize the role of oral microbiota in peri-implant health and disease by determining the composition of the oral bacteriome and mycobiome from subgingival dental plaque, cytokine profile in the crevicular fluid, and to determine if there are any relationships between the oral microbiota, cytokine profile and peri-implant health and disease. Methods: Gingival crevicular fluid and subgingival plaque samples were collected from 20 periodontally healthy patients with healthy implants [Group H] and 9 periodontally healthy patients with peri-implantitis [Group P]. Eight IL-1β, IFN-γ, IL-2, IL-4, IL-6, IL-8, IL-10, and TNF-α were analyzed in crevicular fluid samples isolated from both groups. 16S rRNA and ITS rRNA amplicon sequencing was performed to detect bacterial and fungal species. Results: No statistically significant difference was found in concentrations of IL-2, IL-8, IL-10, and TNF-α. However, statistically significant differences were observed for IL-4 and IL-6. Alpha diversity analysis showed a significant difference between the groups H - Implant vs. P - Tooth and P - Implant vs. P - Tooth. Significant differences in species abundances were also observed between Group H and Group P. Candida parapsilosis and Aspergillus restrictus were significantly enriched in the Group P. Conclusions: To the best of our knowledge, this is the first time Aspergillus restrictus is related to peri-implantitis. Moreover, we found that the relative abundance of Candida parapsilosis is significantly higher in peri-implantitis sites. Our findings further challenge the concept that peri- implantitis is a bacterial disease with specific bacterial pathogens and strengthens the idea that bacterial invasion happens secondary to bone loss because of not very well understood processes such as foreign body reaction.