Objective: To identify dominant pathogens in the periapical lesions associated with persistent apical periodontitis. Methods: Thirty-three root-filled teeth with persistent apical periodontitis referred for surgical treatment were selected. Microbial samples were collected from the periapical lesions during apical surgery. Microbial identification was performed with species-specific primers prepared according to the sequence analysis data using a 16S rRNA technique. Results: Among the 33 cases, in 5 cases none of the target species were detected, 6 cases showed the presence of only one species, and 22 cases showed more than two species. Porphyromonas endodontalis (45% of sample) was the most commonly detected dominant microbial species in the study sample, followed by Actinomyces viscosus (42%), Candida albicans (36%) and Porphyromonas gingivalis (27%). Fusobacterium, Actinomyces israelii and Enterococcus faecalis were also detected in 27%, 21% and 15% of the sample, respectively. The most frequently isolated species, P. endodontalis, was in most cases detected together with Actinomyces (14 cases) and P. gingivalis (6 cases). None of the lesions analysed in the present study contained Prevotella intermedia. There was no correlation in relation to the presence of sinus tracts and the bacterial species. Conclusion: A mixed population of pathogens was found in the endodontic lesions associated with persistent apical periodontitis. P. endodontalis, A. viscosus, C. albicans and P. gingivalis were the dominant species identified. Keywords: bacteria, microbiology, persistent apical periodontitis, 16S rRNA