Objectives: This study evaluates the clinical and microbiological effect of Bifidobacterium probiotic gel as an adjunctive therapy to scaling and root planning (SRP) in chronic periodontitis patients and compering this effect with Chlorhexidine gel. Materials and Methods: Thirty chronic periodontitis patients (18 females, 12 males, aged between 30 and 50 years) were involved in the study. They were classified into 3 groups randomly. 1^st group composed of 10 patients who received SRP associated with the subgingival application of Bifidobacterium probiotic gel, 2^nd group composed of 10 patients who received SRP associated with the subgingival application of Chlorhexidine gel and 3^rd group composed of 10 patients who received SRP only. Local drug delivery was applied once weekly for six weeks. All patients were evaluated clinically by measuring periodontal parameters (Plaque Index, Gingival Index, Probing Pocket Depth and Clinical Attachment Level) , and microbiologically by culturing plaque samples anaerobically for detection of total bacterial count, p.gingivalis & p.intermedia counts at baseline and six weeks after periodontal treatment. Results: All periodontal parameters (PI, GI, PPD and CAL), total bacterial count in addition to p.gingivalis & p.intermedia counts were reduced significantly after six weeks among all the groups. However by comparing in between groups there was significant difference in p.gingivalis & p.intermedia counts between groups 1&3 also between groups 2& 3. Conclusion: The local application of Bifidobacterium probiotic gel offers a promising therapeutic approach in periodontal treatment as adjunct to SRP.