Objective: To investigate the distribution of fimA and kgp genotypes as well as the common genotype combination of Porphyromonas gingivalis (Pg) in infected root canals of primary apical periodontitis for virulent isolates screening in future. Methods: Thirty-four samples harboring Pg were selected from infected root canals of primary apical periodontitis from patients of the Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine from June 2013 to September 2015. FimA type-specific primers were used to amplify the samples, revealing the distribution of various fimA genotypes. The genotypes of kgp were obtained by using Mse Ⅰ restriction endonuclease. The prevalence of each genotype and common genotype combinations were then calculated. Pearson's chi-squared test was performed to analyze the correlation between genotype combinations and clinical symptoms and major signs of apical periodontitis. In addition, the bioflim architectures between Pg isolates with different fimA and kgp genotype combinations were observed compared using confocal laser scanning microscope. Results: Among the 34 Pg-positive samples, fimA Ⅱ was the most prevalent genotype [47% (16/34)] followed by fimA Ⅰ [26% (9/34)], while fimA Ⅴ was detected in only one sample. The prevalence of kgp Ⅰ [56% (19/34)] was slightly higher than that of kgp Ⅱ [44% (15/34)]. Both fimA Ⅱ+kgp Ⅰ and fimAⅡ+kgp Ⅱ were the most prevalent genotype combinations [24% (8/34) each]. No significant correlation was found between specific genotype combination and such major clinical manifestations as gingival swelling and sinus tract of dental origin (P>0.05). Three Pg isolates with different genotype combinations were acquired. Isolate A (fimAⅠ+kgpⅠ) formed densest biofilm, while the biofilm of isolate C (fimAⅤ+kgp Ⅰ) was much looser. The biofilm feature of isolate B (fimAⅢ+kgp Ⅱ) fell in between A and C. Conclusions Pg with fimA Ⅱ was most frequently detected in infected root canals of primary apical periodontitis. The prevalence of Pg with kgp Ⅰ was slightly higher than that with kgp Ⅱ, and fimAⅡ+kgp Ⅰ as well as fimA Ⅱ+kgp Ⅱ were the commonest genotype combinations. According to the comparison of Pg biofilms formed by clinical isolates, it might be possible that different genotype combinations may lead to distinct biofilm architectures.