Chronic periodontitis (CP) and peri-implantitis (PI) are multifactorial diseases of tooth and implant supporting apparatus. Bacterial invasion and consequent host immune response seem to play a role in relevant pathogenesis. The structural differences between tooth and implant pose preferential biofilm colonization. This study was aimed to compare the prevalence of bacteria in CP and PI. Clinical and radiographic examination performed over 69 individuals referred to Shahid Beheshti Dental School (Tehran, Iran) and four groups categorized: CP (n=22), HP (n=21), PI (n=13) and HI (n=13). The mean age was 45.6 years, 55% of participants were female and 45% were male. Bacterial samples were collected by paper point method and transferred to Institute of Odontology, University of Gothenburg (Gothenburg, Sweden) for checkerboard DNA-DNA hybridization. Kruskal-Wallis and Mann-Whitney U tests were used to compare distribution of bacteria in four groups. Significant differences were observed for T. forsythia, P. intermedia, C. rectus, P. endodontic, P. gingivalis, T. denticola and P. tannerae (P<0.05). The most prevalent bacteria in CP and PI were T. forsythia and P. gingivalis, respectively. In conclusion, bacterial prevalence differs significantly between tooth and implant. The most prevalent bacteria in Iranian subpopulation do not necessarily bear a resemblance to other populations. The type of implant surface may influence the biofilm. Other studies should be conducted to corroborate these findings.