This study aimed to determine the prevalence and diversity of archaea and select bacteria in the subgingival biofilm of patients with peri-implantitis in comparison to patients with unaffected implants and patients with periodontitis. Samples of subgingival biofilm from oral sites were collected for DNA extraction (n = 139). A 16S rRNA gene-based polymerase chain reaction assay was used to determine the presence of archaea and select bacteria. Seven samples were selected for direct sequencing. Archaea were detected in 10% of samples from peri-implantitis sites, but not in samples from the unaffected dental implant. Archaea were present in 53% and 64% of samples from mild and moderate/advanced periodontitis sites, respectively. The main representative of the Archaea domain found in biofilm from periodontitis and peri-implantitis sites was Methanobrevibacter oralis. The present results revealed that archaea are present in diseased but not healthy implants. It was also found that archaea were more abundant in periodontitis than in peri-implantitis sites. Hence, the potential role of archaea in peri-implantitis and periodontitis should be taken into consideration.