Introduction: Cassia species (Caesalpinaceae) is a medicinal plant used in traditional Indian medicine for various ailments. In this study, three different bioactive compounds of two medicinal plant species Cassia tora and Cassia fistula were obtained and their antimicrobial properties were compared and evaluated against S.mutans serotype C (ATCC25175) and were conducted as a triple-blind study to identify their effectiveness. Aim: The study aims to evaluate and compare the antimicrobial properties of three different Bioactive Compounds of Cassia species and 0.2% chlorhexidine against S. mutans serotype C (ATCC 25175). Results: All the Bioactive Compounds had good antimicrobial activities based on their zones of inhibition; the highest zone of inhibition in mm was formed by Extract 8 which was Cassia Flower extract having a mean inhibitory zone of 9.93mm +0.76. Stastatistical analysis of the results with Kruskal Wallis and Mann Whitney Post Hoc test proved that at any concentration of Extract 8 the inhibition results are comparable to that of 0.2% chlorhexidine with p=0.05. The results confirmed the antimicrobial potential of the Bioactive Compound of Cassia Flower and hence it can be used as a preventive means for dental caries. Conclusion: The Bioactive Compound of Cassia Flower extract derived from cassia plants are only required in minute quantities as compared to their crude extracts. The study confirmed the antimicrobial potential of the plant at different concentrations can be used as preventive and therapeutic measures in preventive dentistry and due to its reduced potency can be used in children effectively.