Background: Dental plaque is a microbial biofilms that can be the source of various oral diseases. Objectives: This study aimed to investigate the synergistic anti-biofilm effect of chlorhexidine (CHX) and propolis aqueous extract on the Streptococcus mutans and Staphylococcus aureus. Methods: In this study (performed Oct. 2021), the minimum biofilm inhibitor concentrations (MBIC) and the minimum biofilm eradication concentrations (MBEC) of CHX 0.2% and propolis aqueous extract were determined against S. mutans and S. aureus (were prepared from the cell bank of Pasteur Institute of Iran). Also, the in vitro synergistic effect of these two compounds on the inhibition and eradication of biofilm formation of studied bacteria were evaluated using the checkerboard method. Results: The results showed that the MBIC of chlorhexidine for both S. aureus and S. mutans was 125 μg/ml and the MBIC of propolis aqueous extract was 937.5 and 3750 μg/ml, respectively. Also, MBEC chlorhexidine for S. aureus and S. mutans was 250 and ≥500 μg/ml and MBEC propolis 1875 and ≥7500 μg/ml, respectively. The results showed that combining the two substances showed a synergistic effect in inhibiting biofilm formation (p≤0.05) while they had an indifferent effect on biofilm eradication. Conclusions: This study concluded that although CHX is one of the most common and important oral disinfectants in oral diseases, propolis may also be used as an alternative mouthwash with reliable natural antimicrobial properties or with CHX as a moderator of its side effects.