Aim: This study evaluates the clinical and microbiological effect of miswak and chlorhexidine gel on subgingival microbiota. Subjects and Methods: A full mouth randomized controlled clinical trial that carried out on 45 patients of both sex with mild to moderate chronic periodontitis. Selected patients were classified randomly into three equal group. After receiving the basic periodontal therapy group I used miswak 5 time a day (in accordance with the religious tradition), group II used CHX gel with tooth brush twice time daily, group III used tooth brush alone twice time daily. They evaluated clinicaly by Gingival Index, Plaque Index, Propping Depth and Attachment level at base line, after scalling and root blanning, one week, one month and finally after three month of using of each method, and microbiologically for detection and assessment of P.gingivalis at base line , after scalling and root blanning, one week, one month and finally after three month. Resultes: The present study exhibit that miswak more effective than tooth brush, as antimicrobial aginist p. gingivalis. There was no significant difference in the efficacy of miswak and CHX. Conclusion:  Miswak more effective than tooth brush, as antimicrobial agonist.