Objective: Pomegranate peel extract (PPE) and guava leave extract (GLE) were used for centuries and their therapeutic abilities were reported. Hence, this study was conducted to evaluate and compare the antimicrobial effect of mouthwashes prepared from pomegranate peel and guava leave extract on oral Streptococcus mutans (S. mutans) count in healthy subjects. Subject and methods: A total of one hundred healthy children aged between 6-12 years were enrolled in this study and equally divided into five equal groups (n=20) according to mouth rinse type used in this study. Group 1 used 2% chlorhexidine (CHX) mouthwash; group 2 used 10 % PPE mouthwash; group 3 used 15 % PPE mouthwash; group 4 used 10 % GLE mouthwash; while group 5 was use15 % GLE mouthwash. Samples of Saliva were collected after mouth rinsing at two-time intervals; immediately after mouth rinsing and 2 hours after rinsing. Mitis Salivarius agar medium was used to determine S. mutans count. Results: The results revealed that S. mutans count recorded a marked significant reduction in all studied groups immediately after mouth rinsing, then S. mutans count was increased significantly in all groups after 2 hrs. The lowest S. mutans count was recorded with the CHX group followed by15 % and 10% PPE groups respectively. While the lowest performance was observed in GLE 15% and 10 % groups respectively. Conclusions: The use of PPE mouthwash has a higher antimicrobial effect when compared to GLE in both concentrations.