Background: The rapid emergence and spread of multidrug-resistant Staphylococcus aureus (MRSA), especially strains isolated from wounds, represent a major clinical challenge worldwide. This study aims to elucidate the molecular basis of eugenol’s activity by investigating its binding interactions with key therapeutic targets in S. aureus, also evaluating the antibacterial effect of Clove extract on pathogenic S. aureus. Methods: Swabs from wound infection were taken and cultured on Blood, MacConkey and mannitol agar, then incubated in 37 C for 24 hours. The obtained S. aureus isolates then used for plant extract antibacterial tests. The ethanolic extract of Clove plant (Syzygium aromaticum) by mean of three concentrations (25, 50 and 75 mg/dl) were used to evaluate their antibacterial efficiency against Staphylococcus aureus that isolated from wound infection. By using the molecular docking, the molecular basis of eugenol’s activity were elucidate by investigating its binding interactions with key therapeutic targets in S. aureus: Penicillin-binding protein 2a (PBP2a, PDB ID: 1VQQ), Beta-lactamase (PDB ID: 6WGR), Dihydrofolate reductase (DHFR, PDB ID: 6PR6), and the CHAP domain of lysin L1 (PDB ID: 11CF). Results: The results showed that large inhibition diameter (27 mm) was observed surrounding the high concentration of plant extract (75 mg/dL), followed by 50 mg/dl with (23mm), and 20 mg/dl (18mm). The negative control didn’t showed any zone of inhibition. The molecular docking study revealed moderate to good binding affinities of eugenol with the selected S. aureus proteins, with Vina scores ranging from -5.5 to -6.2 kcal/mol. Eugenol exhibited the strongest binding at -6.2 kcal/mol Conclusion: The high concentration of Clove extract exhibits good efficiency against S. aureus. Molecular docking supports these findings by investigating favorable interaction between Eugenol and bacterial essential protein. These revealed that Clove plant with their bioactive compounds has a potential role as antibacterial agents against pathogenic bacteria.