The purpose of this review article is to assess systematically the available scientific evidence about difference in microbiota of apical periodontitis in root canals during time and its antibiotic susceptibility. The study of publications was produced in the electronic databases such as Google Scholar, PubMed during a systematic review of the literature. Included articles contain information about microorganisms in the root canal system of different forms of apical periodontitis. The publica-tion date criterion was selected from January 2000 to December 2012. Overall 52 articles were reviewed. After analyzing the literature for inclusion criteria, the total number of publications has become 10. According to literature data, bacteria located in the apical root canal system potentially par-ticipate in the pathogenesis of acute and chronic, primary and secondary apical periodontitis. Anaerobic bacteria are dominated with similar proportion of gram-negative and gram-positive microorganisms. During twelve years there were some changes in microbiota’s community. The most common ones in early 2000 were Streptococcus spp. and Fusobacterium nucleatum. Then in 2008 the leading positions were taken by Olsenella uli, Eikenella corrodens and Porphyromonas endodontalis. Beta-lactams, macrolides, metronidazole are the choices for antibiotic therapy of apical periodontitis, depending on its microbial biocenosis. All authors contributed equally to the writing of the article. © 2022, Yerevan State Medical University. All rights reserved.