The aim of the present study is to assess the efficiency of diode laser as an adjunctive therapy with non-surgical treatment on the red complex pathogens in chronic periodontitis using Polymerase chain reaction (PCR). Materials and Methods Study Design: The selected patients were divided into two groups: Group A: included 10 patients, which were treated with conventional supra and sub gingival scaling and root planning. Group B: included 10 patents, which treated with conventional supragingival and subgingival SRP and diode laser therapy. Bacterial sampling and analysis: Subgingival Plaque samples were obtained from 4 sites in each subject, the mesial surfaces of one of the selected teeth. The same sites were examined at baseline and at the follow-up periods. A paper point was inserted in each pre-selected periodontal pocket for 30 seconds than transformed to the plastic epindorphe tube. Subgingival plaque samples were collected from the same sites at baseline and at 2 weeks and 6 weeks post periodontal and laser treatment. Identification and quantification of P.g ,Ta.f and Tr.d and total bacterial load were evaluated using real-time PCR technique (Kamma et al., 2006). The test group patients were subjected to conventional therapy (supragingival scaling and subgingival debirdement) and Laser. Regarding the clinical periodontal evaluation our results showed that after 2 weeks of therapy there was significant improvement in the Gingival index, plaque Index, attachment loss and level of attachment in both groups of the mouth. After 6 weeks; the previously mentioned clinical parameters were still significantly better in the laser group where scaling and root planning was done plus low level Laser therapy. Results of microbial evaluation showed that P. Gingivalis, T Denticolaand T Forsaitha nd decreased significantly after treatment and this decrease extended to the 2 week in the SRP th alone group while it extended up to the 6 week in the SRP+LAS group. Conclusion: Scaling and root planning was effective in improving clinical and microbiological parameters in patients with chronic periodontitis and this effect continued for two weeks after therapy to sex weeks. Scaling and root planning plus laser therapy was better than scaling and root planning alone in patients with chronic periodontitis and this effect continues to be significant up to 6 weeks after therapy. P gingivalis was the most common organisms found in our study patients and T forsythia and Tr denticoola were the least common organism. Laser therapy could be used for the treatment of periodontitis as a complementary therapy not to replace mechanical intervention.