Sortases are a family of Gram-positive transpeptidases responsible for anchoring surface protein virulence factors to the peptidoglycan cell wall layer. In Staphylococcus aureus, deletion of the sortase isoforms results in marked reduction in virulence and infection potential, making it an important antivirulence target. We examined the effects of naturally occurring flavonols on recombinant sortase A (SrtA) and B (SrtB) prepared from S. aureus ATCC6538p and found that these compounds inhibited the activity of sortases, without exhibiting antibacterial activities. Among the flavonols tested, morin, myricetin, and quercetin exhibited strong sortase inhibitory activities (SrtA IC₅₀: 37.39—52.70 μM, SrtB IC₅₀: 8.54—36.89 μM). The fibrinogen cell-clumping activity data highlight the potential of flavonols for the treatment of S. aureus infections via inhibition of sortase.