Objectives: To assess the microbiota at implants diagnosed with peri-implantitis, implant mucositis, or being clinically healthy. Material and methods: Clinical and microbiological data were collected from 213 subjects (mean age: 65.7 +/- 14) with 976 implants in function (mean: 10.8 years, SD +/- 1.5). Forty species were identified by the checkerboard DNA-DNA hybridization method. Results: Implant mean % plaque score was 41.8 +/- 32.4%. Periodontitis defined by bone loss was found in 44.9% of subjects. Implant mucositis was diagnosed in 59% and peri-implantitis in 14.9% of all cases. Neisseria mucosa, Fusobacterium nucleatum sp. nucleatum, F. nucleatum sp. polymorphum, and Capnocytophaga sputigena dominated the implant sub-mucosal microbiota and the sub-gingival microbiota at tooth sites. Implant probing pocket depth at the implant site with the deepest probing depth was correlated with levels of Eikenella corrodens (r=0.16, P < 0.05), the levels of F. nucleatum sp. vincentii (r=0.15, P < 0.05), Porphyromonas gingivalis (r=0.14, P < 0.05), and Micromonas micros (r=0.17, P=0.01). E. corrodens was found in higher levels at implants with mucositis compared with implant health (P < 0.05). Subjects who lost teeth due to periodontitis had higher yields of F. nucleatum sp. vincentii (P < 0.02) and N. mucosa (P < 0.05). Independent of implant status subjects with teeth had higher levels of P. gingivalis (P < 0.05), and Leptotrichia buccalis (P < 0.05). Conclusions: At implant sites studied, few bacteria differed by whether subjects were dentate or not or by implant status.