The purpose of this study was to investigate the epidemiology of putative pathogens in root canals with apical periodontitis and to determine the associations among the putative pathogens. Eighteen symptomatic and 20 asymptomatic teeth from 36 subjects were studied. This research was performed with polymerase chain reaction and hybridization using rRNA-based oligonucleotide probes. The most frequently found species was Fusobacterium sp. (68.4%), followed by Peptostreptococcus micros (44.7%) and Porphyromonas gingivalis (26.3%). Sixteen teeth (42.1%) contained one or more species of the selected black-pigmented bacteria. Bacteroides forsythus and Treponema sp. were detected in 8 teeth and 6 teeth, respectively. Among the analyzed bacteria, significant relationships were shown in the combination of B. forsythus/P. gingivalis and Treponema sp./P. gingivalis. There was no significant association between any bacteria and any symptoms.