Abstract The aim of this study was to i) evaluate the prevalence of P. gingivalis and the genotypes fim A I, Ib, II, III, IV, and V in Brazilian patients with periodontitis stage III and IV, grades B and C, ii) compare periodontitis grades B and C with regard to the prevalence of P. gingivalis and fim A genotypes, and iii) correlate the presence of these pathogens with clinical periodontal variables. Two samples of subgingival biofilm were collected from the interproximal sites with the greatest clinical attachment loss (CAL) of each patient (grade B = 38; grade C = 54) and submitted to polymerase chain reaction (PCR) for the identification of P. gingivalis and fim A genotypes. The collected periodontal clinical parameters included gingival index, plaque index, probing depth (PD), bleeding on probing (BoP) and CAL. P. gingivalis was present in 61.96% of the samples, but more prevalent in patients with grade C periodontitis (p = 0.048) and higher CAL (p < 0.001), PD (p < 0.001), and BoP (p = 0.01) values, and at sites with high CAL values (p = 0.01). The fim A II genotype was more prevalent in patients with greater mean PD (p = 0.04) and a higher proportion of bleeding sites (p = 0.006). Thus, in this sample of Brazilian periodontitis patients, the presence of P. gingivalis was associated with grade C periodontitis and periodontal destruction, while the fim A II genotype was associated with increased PD and BoP, supporting the notion that P. gingivalis fim A II is an important virulence factor in periodontal tissues.