Aim: Streptococcus mutans and Lactobacillus acidophilus is one of the most common oral microflorae responsible for the formation and progression of dental caries respectively. Patients undergoing orthodontic treatment have alterations in their micro flora due to increased accumulation of debris around orthodontic auxiliaries. With our previous study we have found that there was significant antibiotic effect for watermelon juice against lactobacillus. The aim of the currentstudy is to find the effect of ethanolic extract of Citrullus lanatus(watermelon) against oral microflora such as Lactobacillus acidophilus and Streptococcus mutans in patients undergoing orthodontic treatment. Materials and methodology: Ethanolic extract of watermelon was prepared. Three different concentrations of the extract were used to find its antibiotic effect against oral microflora such as lactobacillus and streptococcus mutans. Paper discs incorporated with the extract were incubated in freshly prepared colonies of lactobacillus acidophilus and streptococcus mutans. After incubation period the culture plates were examined for antibiotic sensitivity. Results: Results showed that there was no decrease in the bacterial colony count in the culture plate containing three different concentrations of ethanolic extract of watermelon. Conclusion: Though watermelon juice had significant effect against lactobacillus, the Ethanolic extract of Citrullus lanatus had no significant antibacterial effect against lactobacillus acidophilus and streptococcus mutans in patients undergoing orthodontic treatment.