Abstract: In the present study the Checkerboard DNA-DNA hybridization technique was used to identify bacteria in persistent periapical lesions and recurrent marginal periodontitis. A second aim of the study was to investigate if two different flap designs during surgery would influence the detection rate of bacterial DNA in periradicular tissue.The study included 68 patients. 24 patients had the diagnosis recurrent marginal periodontitis (group A), and 44 patients had root-filled teeth with persistent apical periodontitis (Group B). The group with apical periodontitis was divided into two subgroups, B1, and B2. In B1, which included 23 patients, a marginal incision was performed during surgery, and in B2, including 21 patients, a submarginal incision was applied. Bacterial DNA was identified in all samples from the three groups using 20 different whole genomic probes. The mean number of species detected was 13. 3 in Group A, 11. 4 in group B1 and 9. 7 in group B2. Porphyromonas gingivalis, Prevotella nigrescens, Treponema denticola, Actinomyces israelii, Actinomyses viscosus, Peptostreptococcus micros, E ubacterium saburreum and Treponema socranskii dominated in all three groups.P. gingivalis was present in 83% of the lesions in group A, 78% in group B1 and in all lesions in B2. T. denticola was present in 95% in group A and in all lesions in group B1 and B2. The third bacteria in the red complex , T. forsythia was present in 79% in group A, in 52% of the lesions in group B1 and 39% in group B2. Species present in high numbers (> 106 cells) in group A (in more than three lesions) were: P. gingivalis, A. actinomycetemcomitans, T. denticola, P. nigrescens, F. nucleatum ssp polymorphum, T. socranskii ssp. socranskii, Peptostreptococcus micros, S. intermedius. E. saburreum, T. denticola. P. nigrescens were present in high numbers in group B1 and T. denticola and P. nigrescens in group B2.A consortium of different species, both anaerobic and facultative anaerobic species, were identified in recurrent marginal periodontitis and in persistent periapical lesions.