Background: The success of endodontic treatment is directly related to the decrease in the number of root canal microorganisms. The present study was conducted to determine the microbial flora in infected root canals. Materials & Methods: The present study was conducted on 92 single rooted teeth of both genders. Bacterial samples were evaluated by means of an advanced microbiological technique specific for anaerobic species. Results: Out of 92 samples, 64 were from necrotic pulps (primary infection) and 28 from unsuccessful RCT (secondary infection). The difference was significant (P< 0.05). Common bacteria isolated from root canals was Peptostreptococcus in 20.3% followed by Streptococcus in 18.1%, Porphyromonas in 15.5%, Enterococcus in 12.4%, Staphylococcus in 10.2%, Prevotella in 7.1%, Actinomyces in 6.5%, Veillonella in 5.9% and Eubacterium in 4%. The difference was significant (P< 0.05). Conclusion: Authors found that common bacteria isolated from pulp chambers and root canals were Peptostreptococcus, Streptococcus, Porphyromonas and Enterococcus. Key words: Streptococcus, Enterococcus, Bacteria