The aim of this study was to i) evaluate the prevalence of P. gingivalis and the genotypes fimA 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 fimA 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 fimA 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 fimA 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 fimA II genotype was associated with increased PD and BoP, supporting the notion that P. gingivalis fimA II is an important virulence factor in periodontal tissues.