Statement of the Problem: Dental caries is one the most prevalent diseases that affects humans throughout their lives. Streptococcus mutans (S. mutans) is recognized as the most important microorganism during tooth cariogenicity. Reducing this germ in oral cavity can reduce the rate of tooth decays in humans.Purpose: The present study compared the antimicrobial activity of ethanolic extract of Peganum harmala L. seeds and 0.2% chlorhexidine on S. mutans.Materials and Method: Agar diffusion technique and micro broth dilution method were employed to test the antimicrobial effects of these two agents on S. mutans. Moreover, the cytotoxicity of ethanolic extract of P. harmala was studied on Vero cells by MTT (thiazolyl blue tetrazolium dye) colorimetric method. The data were analyzed with descriptive methods.Results: Concentrations of 50, 25, and 12.5 mg/mL of the extract made inhibition zones of bacterial growth around the wells; but, lower concentrations could not inhibit the growth of S. mutans. Besides, the antimicrobial effect of 0.2% chlorhexidine was more than 50 mg/mL of the extract. Minimum inhibitory concentration (MIC) of the extract on S. mutans was 1.83±0.6 mg/mL and minimum bactericidal concentration (MBC) was 4.3±1 mg/mL. The MIC and MBC for 0.2% chlorhexidine were reported to be 0.19 mg/mL, and 0.78 mg/mL, respectively. The extract concentrations more than 0.5 mg/mL were toxic and caused more than 50% Vero cell death.Conclusion: Despite the remarkable antimicrobial effects of high concentrations of P. harmala on S. mutans, high cell toxicity of this plant would restrict its in vivo therapeutic use.