This study assessed the levels of tumor necrosis factor-α (TNF-α), prostaglandin E2 (PGE2), receptor activator of nuclear factor kappa B (RANK), RANK ligand (RANKL), osteoprotegerin (OPG), and levels of Fusobacterium nucleatum, Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, and Streptococcus oralis in areas where airborne particle-abraded, large-grit, acid-etched (SLA), fluorine-modified, and anodized implant surfaces are used. A total of 71 implants from 37 patients were assessed, grouped according to the surface characteristics of the implants: SLA surface (Group 1), fluorine-modified surface (Group 2), and anodized surface (Group 3). The following clinical indices were measured: Gingival Index (GI), probing depth (PD), bleeding on probing (BOP), clinical attachment level (CAL), and keratinized tissue width (KTW). Peri-implant sulcus fluid and subgingival plaque samples were also collected. Commercial enzyme-linked immunosorbent assay (ELISA) kits were purchased for measuring TNF-α, PGE2, RANKL, RANK, and OPG. Real-time quantitative polymerase chain reaction (PCR) was used to detect P intermedia, T forsythia, T denticola, F nucleatum, P gingivalis, and S oralis levels in the subgingival biofilms. The groups showed no statistically significant differences in GI, PD, BOP, CAL, KTW, or peri-implant status. The total amounts of PGE2, TNF-α, RANKL, RANK, and OPG and the RANKL/OPG ratio were not significantly different between groups. F nucleatum, T forsythia, P intermedia, P gingivalis, and T denticola were significantly higher in Group 3 implants. DNA concentrations of S oralis were higher in Group 2. Within the limitations of this study, SLA and fluorine-modified implant surfaces may be more clinically successful than anodized-surface implants.