The use of chemical devices for non-surgical periodontal therapy has led to new treatment strategies aimed primarily at controlling infection. Over the last few years, titanium dioxide (TiO2) with monovalent silver ions (A) covalently linked and added to benzalkonium (B) (named TIAB) has been subjected to medical studies, especially in dermatology. The purpose of the present study was to assess the effect of TIAB on the red complex bacteria using Polymerase Chain Reaction (PCR) for microbiological analysis. A split mouth study was conducted, and 10 subjects were enrolled. TIAB as topical medication was placed at study sites after scaling and root planing. Sub-gingival plaque samples were collected after 2 weeks, and red complex micro-organisms were studied using PCR. SPSS program was used for statistical purposes and a paired sample correlation was performed at the end of the observation period between treated and untreated sites. The results showed statistically significant reduction of red complex organisms in the study compared to the control group. TIAB can be used as an effective local drug along with supportive periodontal therapy in treatment of chronic periodontitis.