In aggressive periodontal disease A.a and P.g are able to infect periodontal sites by adhering to the cells (particularly epithelial cells) or to surface of the tooth, by competing effectively with the large resident microbial population, and by overcoming cellular and humoral defense mechanisms. Because of the high virulence and destructive nature this periodontal pathogens,the dental practitioner needs to employ systemic antibiotics in addition to surgical and/or nonsurgical therapy to treat severe forms of periodontitis in which A.a and P.g are directly involved.Moxifloxacin is a fourth-generation synthetic fluoroquinolone antibacterial agent, that is marketed worldwide (as the hydrochloride) under the brand names Avelox, Avalox, and Avelon. It is a broad-spectrum antibiotic, and it was found to have good antibacterial activity against periodontal pathogen. Thirty patients with both localized and generalized aggressive periodontitis were used in the current study and divided into three groups; the tested group that included ten patients who received Moxifloxacin (400 mg once per day for 10 days) in conjunction with SRP and the control groups that included ten patients treated with combination of augmentin/ metronidazol and ten patients treated with SRP alone.In each subject, subgingival plaque samples were collected from the four deepest defects of each quadrant at the base line and at 3& 6 months after therapy and were used for evaluation of their content of two subgingival microbial species P.g and A.a using DNA probes.The results of the quantitative PCR technique revealed a significant reduction in the A.a count (100%) in augmentin/metronidazol treated group and (82.2%) reduction for moxifloxacin treated group, while SRP alone showed a percentage reduction of only (9.2%). As for P.g, moxifloxacin group showed the highest significant percentage reduction in log10 values of P.g (69.8%), followed by augmentin & metronidazole group (54.2%), and only (3.6%) for SRP alone. The results obtained suggested that moxifloxacin as an adjunct to SRP represents a viable approach to treat aggressive periodontitis. It resulted in clinical as well as microbiological improvement over 6 months.