Introduction: Dental malocclusions are one of the most common oral health problems and are associated with difficulties in maintaining oral hygiene. Mouthwashes may affect the plaque formation and reduces the number of streptococcus mutan count. Aims and objectives: To evaluate the effect of alcoholic, non-alcoholic and organic mouthwash on the level of streptococcus mutans in the during the early phase of orthodontic treatment. Material and Methods: 120 patients aged between 12 -20 years who visited the department were selected and randomly allocated into four l groups. Microbial records and periodontal parameters obtained before bonding (T0), 1 week (T1), 2 week (T2), 3 week (T3), and 4 week (T4) after bonding and colonies were counted under Stereomicroscope and the results were expressed as colony forming units per milliliter and analysis was done using the SPSS (p<0.05). Conclusion: On comparison it was found that both organic mouthwash (Hiora) and non alcoholic mouthwash (Rexidin Plus) showed comparable clinical and microbiological results.