Even though most studies consider strict anaerobe Gram-negative bacteria as the main factor associated with peri-implantitis, other studies have identified other microorganisms present in implants related to peri-implant disease that have the ability to reduce the effectiveness of treatment, such as Candida spp., Enterococcus faecalis and Pseudomonas aeruginosa. Therefore, microbiologic diagnosis is important for the success of implant treatment. The main goal of this study was to detect Candida spp., E. faecalis and P. aeruginosa in the peri-implant and periodontal subgingival plaque in the presence or absence of disease and to relate the presence of these microorganisms with demographic data, hygiene habits, the type of implant connection and endodontic treatment. The study population consisted of 20 patients that filled out a questionnaire regarding gender, age, systemic diseases and oral hygiene. The peri-implant and periodontal subgingival plaque from an adjacent tooth, both with and without disease, were analysed for the presence of these three opportunistic pathogens. Microbiological analysis revealed a higher prevalence of E. faecalis in patients with and without periodontal and peri-implant disease. Candida spp. was identified in a higher degree in cases with disease, and P. aeruginosa was mostly detected in peri-implantitis. The detection of these three pathogens suggested a possible means of transmission of infection from adjacent teeth to implants, with the implant design associated with rehabilitation being a primary cause of pathogen growth. Although this study did not relate pathogen growth directly to periodontal disease, the high colony forming unit per millilitre (CFU/mL) values of E. faecalis may reveal an aetiological role of this bacterium in peri-implantitis.