Background: Caries is one of the most commonly affecting diseases of the oral cavity. There are many methods of removing caries but prevention is always better than cure. Mouthwash is a well studied chemotherapeutic agent. Though many mouthwashes are available in the market, the quest for a good and effective mouthwash is still there. Acacia nilotica and thymus vulgaris have been used in the present study as mouthwash. Materials and methods: Mouthwashes have been prepared using Acacia nilotica and Thymus vulgaris and the anti microbial activity and cytotoxicity of the mouthwashes have been evaluated against various oral microbes and compared with commercially available chlorhexidine mouthwash. Results: Acacia and Thyme have both shown good antimicrobial and less cytotoxic activity. Synergistic activity is shown by both the mouthwashes. Conclusion: Acacia nilotica and thymus vulgaris can be used as effective mouthwash.