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,Synergistetescluster B,Leptotrichia, Megasphaera,Anaeroglobus geminatus, andTannerella forsythiadisplayed significantly differential abundances between the groups. Whereas abundances ofMegasphaeraandA. geminatuswere significantly increased in the RA group, onlyPorphyromonas gingivalisdisplayed significant correlations with plaque scores, bleeding on probing, and RF-IgA. RA patients displaying RF-IgA levels >75 IU/mL exhibited five-fold more abundantP. gingivalislevels than patients below the threshold. This association with RF-IgA levels appeared even more pronounced, by six-fold moreP. gingivalis(P = 0.025), in patients with a DAS-28 score >3.2, indicative of moderate/very active RA. Conclusions Unattached GCF bacteria may mediate the association between periodontitis and RA, and monitoring the bacterial composition of GCF might inform on RA activity. The role of newly identified bacterial taxa in RA warrants further investigations.