Aim: To do comparative evaluation of antibacterial efficacy of Myristica Fragrans (1%) a novel mouth wash with chlorhexidine (0.2%) mouth wash against salivary Streptococcus Mutans count.Methods: An experimental, in-vivo, parallel group randomized control trial was planned. School going children in the age group of 14-16 years was considered for the study. Twenty four students were selected to take part in the study. Twelve students were randomly allocated to each of the groups. Freshly prepared 1% nutmeg mouthwash and commercially available 0.2%chlorhexidine was used in the study. Results: The streptococcus mutans levels was significantly reduced in both 1% nutmeg mouthwash and in 0.2% chlorhexidine groups (p=0.003). The results showed that the two groups were comparable antibacterial properties against streptococcus mutans (p=0.92). Conclusion: The results showed that the 1% nutmeg herbal mouthwash is an effective agent against streptococcus mutans as chlorhexidine mouth wash after eight days.