Purpose: To determine the effect of mechanical tooth cleaning by toothbrush and dental floss on mutans streptococci in the saliva of preschool children. Materials and Methods: This blinded, randomised controlled clinical trial included 54 3-year-old preschool children with detectable mutans streptococci in saliva. The children were randomly divided into a test and a control group. Dental college students cleaned the teeth of test group participants with toothbrush and dental floss under the indication of a plaque disclosing agent once a day. The control group received no intervention. Dentocult SM Strip mutans (D-SM) strips were used to test the mutans streptococci in saliva. Results: The D-SM test scores declined from 1.82 to 0.95 for the test group after the teeth were cleaned 10 times (P 0.001) and the scores increased to 1.62 after tooth cleaning ceased for 2 weeks (P > 0.05 compared with baseline). The D-SM level of the control group did not change significantly. Conclusion: Meticulous and continuous plaque control with toothbrush and dental floss can decrease the mutans streptococci level in preschool children. However, the effect ceased as the intervention ceased. Keywords: dental flossing, Dentocult SM Strip, mutans streptococci, preschool children, toothbrushing