Background: Periodontitis is a suspected environmental risk factor for the development of rheumatoid arthritis (RA). However, correlation mechanisms between the two pathologies remain elusive. This study examined potential correlations between detached subgingival bacteria collected in gingival crevicular fluid (GCF) and RA parameters. Methods: RA patients (n = 52, F:M = 40:12), patients with Behcet's disease (BD, n = 40, F:M = 29:11) as another systemic inflammatory disease were studied along with a systemically healthy control group (HC, n = 57, F:M = 40:17). All participants were non-smokers. Full mouth periodontal parameters were recorded. RA activity was assessed using the 28-joint Disease Activity Score (DAS-28). Rheumatoid factors (RFs)-IgM and-IgA were measured by ELISA. GCF samples were investigated by means of fluorescent in situ hybridization for 10 different bacterial taxa. Results: The taxa TM7, Synergistetes cluster B, Leptotrichia, Megasphaera, Anaeroglobus geminatus, and Tannerella forsythia displayed significantly differential abundances between the groups. Whereas abundances of Megasphaera and A. geminatus were significantly increased in the RA group, only Porphyromonas gingivalis displayed significant correlations with plaque scores, bleeding on probing, and RF-IgA. RA patients displaying RF-IgA levels >75 IU/mL exhibited five-fold more abundant P. gingivalis levels than patients below the threshold. This association with RF-IgA levels appeared even more pronounced, by six-fold more P. gingivalis (P = 0.025), in patients with a DAS-28 score >3.2, indicative of moderate/very active RA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.