This study evaluated the efficacy of glycone (myricitrin, hesperidin and phloridzin) and aglycone flavonoids (myricetin, hesperetin and phloretin) in inhibiting biofilm formation by Staphylococcus aureus RN4220 and S.aureus SA1199B that overexpress the msrA and norA efflux protein genes, respectively. The minimum inhibitory concentration (MIC) and minimum biofilm inhibitory concentration (MBIC50 - defined as the lowest concentration that resulted in ≥50% inhibition of biofilm formation) of flavonoids were determined using microdilution in broth procedures. The flavonoids showed MIC >1024μg/mL against S.aureus RN4220 and S.aureus SA1199B; however, these compounds at lower concentrations (1-256μg/mL) showed inhibitory effects on biofilm formation by these strains. Aglycone flavonoids showed lower MBIC50 values than their respective glycone forms. The lowest MBIC50 values (1 and 4μg/mL) were observed against S.aureus RN4220. Myricetin, hesperetin and phloretin exhibited biofilm formation inhibition >70% for S.aureus RN4220, and lower biofilm formation inhibition against S.aureus SA1199B. These results indicate that sub-MICs of the tested flavonoids inhibit biofilm formation by S.aureus strains that overexpress efflux protein genes. These effects are more strongly established by aglycone flavonoids.