The study aimed to examine the relationship between the subgingival flora around implants and their periodontal parameters. Plaque samples from 561 implants (279 patients) were analyzed by means of differential phase contrast microscopy and compared with the sample site's probing depth, bleeding tendency on probing, and plaque and gingivitis indices. If possible, one implant with deep and one with shallow pockets were selected within the same patient. The impact of the intraoral exposure time on the microbial composition around the implants was examined cross-sectionally, with the same group of patients. Only tendencies can be detected by the latter, and no concrete conclusions can be drawn. From the clinical parameters, increased probing depth was found to detrimentally increase the proportion of spirochetes and motile organisms, whereas the other parameters were found to be of minor importance. For partially edentulous patients only, there was a tendency for increased proportions of spirochetes and motile organisms the longer the intraoral exposure time. These observations emphasize the importance of the periodontal health of the remaining teeth (as a reservoir of pathogenic microorganisms) in partial edentulous patients rehabilitated by means of implants and indicate the importance of shallow pockets around implants (flap trimming when aesthetics and phonetics allow).