It has been documented that periodontopathic bacteria are also implicated in endodontic infections. 168 rDNA gene-directed PCR was to examine the prevalence of periodontopathic bacteria including Actinobacillus actinomycetemcomitans (Aa), Prevotella intermedia (Pi), Prevotella nigrescens (Pn), Porphyromonas gingivalis (Pg), Porphyromonas endodontalis (Pe), and Treponema denticola (Td) in the root canals of 36 endodontically infected teeth having apical lesions with or without clinical symptoms like pain, swelling, and fistula. 1. In 36 infected root canals, most frequently detected bacterial species was Pg (61.1%), followed by Td (52.8%) and Pe (38.9%). 2. Of 36 infected root canals, Aa was detected in 6 canals (16.7%) of the teeth, all of which showed clinical symptoms. 3. Of 36 infected root canals, Pi and Pn were found in 4 03.9%) and 5 (33.3%), respectively. Notably, prevalence of Pn in the symptomatic teeth was 50.0%. 4. One of black-pigmented anaerobic bacteria (BPB) including Pi, Pn, Pe, and Pg was detected in all of the teeth that showed pain or especially swelling but not fistula. It was, however, found that prevalence of BPB in the asymptomatic teeth or the teeth with fistula was only 40%. 5. Pe and Pg were detected in the teeth regardless of the presence or absence of symptoms. 6. Td was detected in the teeth regardless of the presence or absence of symptoms. High prevalence of BPB in the symptomatic teeth but low in the asymptomatic teeth suggests that BPB may play an important role in the pathogenesis of periapical lesions.