OBJECTIVE: To compare the prevalence and levels of six bacterial pathogens within the subgingival/submucosal microbiota at teeth versus implants with various clinical conditions. MATERIAL AND METHODS: Twenty-two Chinese were included. Four subgingival/submucosal sites were selected for microbiological sampling within each subject, that is, (1) healthy peri-implant tissues; (2) peri-implantitis [PPD ≥ 5 mm, presence of bleeding on probing (BOP) and confirmed radiographic bone loss]; (3) healthy gingiva; and (4) periodontitis (PPD ≥4 mm). Subgingival/submucosal plaque was sampled using paper points. Quantitative real-time polymerase chain reaction (q-PCR) was used to quantify six pathogens, including Porphyromonas gingivalis (P.g.), Treponema denticola (T.d.), Aggregatibacter actinomycetemcomitans (A.a.), Fusobacterium nucleatum (F.n.), Prevotella intermedia (P.i.), and Staphylococcus aureus (S.a.). Counts were log10-transformed. RESULTS: The most commonly detected species were S. a. and F. n., while A. a. and. P. i. had the lowest detection frequency. The detection frequencies of diseased tooth or implant sites for each of the six target species were either equal to or higher than the respective frequencies at the corresponding healthy sites. There were no statistically significant differences for any of the species or clinical sites (P > 0.05, Cochran's Q test). No statistically significant differences in the bacterial loads were found among the four clinical sites; with the exception of F. nucleatum. This was more abundant in periodontitis sites (P = 0.023, Friedman's 2-way anova). Both periodontal and peri-implant sites, irrespective of their health status, were revealed to harbor S. aureus cells. The log10-transformed loads of S. aureus were approximately 3.5 within each of the clinical sites (P = 0.232). This was the highest of the six species analyzed. CONCLUSIONS: Within the same subjects, putative periodontal pathogens were common to both periodontal and peri-implant sites irrespective of health status. The prevalence and levels of P. gingivalis and F. nucleatum were significantly associated with periodontitis, but not with peri-implantitis. A. actinomycetemcomitans was associated with both disease conditions, periodontitis and peri-implantitis, but not with either gingival or mucosal health.