Mouthwashes are used routinely as adjunct to scaling and root planing. Chlorhexidine mouthwash is known as gold standard while Listerine is a widely used essential oil mouthwash. This study was done to evaluate and compare the genotoxic effect of Listerine with Chlorhexidine mouthwash on buccal cells.It was a parallel design study with 20 participants in each group (Group 1: Chlorhexidine mouthwash and Group 2: Listerine mouthwash). Gingival index was recorded and buccal cells scraping were taken at baseline and 3 weeks after use of respective mouthwashes. The buccal cells were assessed for cytotoxicity using micronuclei test (under microscope at 100 x magnification) using Papanicolaou Stain.There was a statistically significant reduction seen in gingival index from baseline to 3 weeks in both the groups (p< 0.001). There was a statistically significant increase in micronuclei count and number of Micronucleated cells in both the groups from baseline to 3 weeks (p< 0.001). The intergroup analysis showed highly significant increase in micronuclei and Micronucleated cells numbers in Chlorhexidine mouthwash group as compared to Listerine group (p< 0.001).After a 3 weeks exposure, Listerine mouthwash showed less cytotoxicity on buccal cells as compared to Chlorhexidine mouthwash.