Background Implants are a predictable and well-established treatment method in dentistry. Nevertheless, looking at possible failures of dental implants, early and late loss have to be distinguished. The intent of the study was to report microbiological findings on the surface of implants with severe peri-implantitis, which had to be explanted. Methods 53 specimens of implants from 48 patients without severe general illnesses have been examined. The groups investigated were implants that had to be removed in the period of osseointegration (early loss, 13 patients with 14 implants) or after the healing period (late loss, 14 patients with 17 implants). The implant losses were compared with two control groups (implants with no bone loss directly after completed osseointegration, two to four months after implant placement (17 patients with 17 implants) and implants with no bone loss and prosthetic restoration for more than three years (5 patients with 5 implants)). Data about the bacteria located in the peri-implant sulcus was collected using amplification and high throughput sequencing of the 16S rRNA gene. Results The biofilm composition differed substantially between individuals. Both in early and late implant loss of Fusobacterium nucleatum , and Porphyromonas gingivalis were found to be abundant . Late lost implants showed higher bacterial diversity and in addition higher abundances of Treponema, Fretibacterium, Pseudoramibacter and Desulfobulbus , while microbial communities of early loss implants were very heterogeneous and showed no significantly more abundant bacterial taxa. Conclusions Specific peri-implant pathogens were found around implants that were lost after a primarily uneventful osseointegration. P. gingivalis and F. nulceatum frequently colonized the implant in early and late losses and could therefore be characteristic for implant loss in general. In general, early lost implants showed also lower microbial diversity than late losses. However, the microbial results were not indicative of the causes of early and late losses.