OBJECTIVE Prevention of peri-implantitis is essential for the success of implant rehabilitation. Infection by periodontopathic bacteria is a major cause of peri-implantitis. The aim of the present study was to identify the source of peri-implant colonization by periodontopathic bacteria. METHODS Twenty-one patients with implants were enrolled in the study. Subgingival plaque samples from the adjacent, occluding, and contralateral natural teeth were collected prior to second-stage surgery. Samples from implant sulci were then obtained 2 weeks later. Detection of periodontopathic bacteria was performed by the polymerase chain reaction. RESULTS The detection rates for Aggregatibacter actinomycetemcomitans, Prevotella intermedia, Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Fusobacterium nucleatum in all subgingival samples from natural teeth were similar to that in the peri-implant sulci. Multiple logistic regression analysis revealed an association between the detection of A. actinomycetemcomitans, Prevotella intermedia, Porphyromonas gingivalis, Treponema denticola, and F. nucleatum in the gingival crevices of adjacent teeth and that of the peri-implant sulcus, but no association for Tannerella forsythia. CONCLUSIONS The present findings suggest that colonization by A. actinomycetemcomitans, Prevotella intermedia, Porphyromonas gingivalis, Treponema denticola, and F. nucleatum at the implant sulcus was affected by these microorganisms in the gingival crevice of adjacent teeth rather than those on occluding and contralateral teeth.