Antimicrobial resistance of methicillin resistant Staphylococcus aureus (MRSA) became on the top list of the serious problems that have a negative impact on public health. Therefore, this study aimed to determine the in vitro antibacterial activities of Nigella sativa (N. sativa) and clove essential oils against multidrug resistant (MDR) methicillin resistant Staphylococcus aureus (MRSA) isolates recovered from different sources with a special reference to their role on the expression of penicillin binding protein (pbp < /em>2) and muscle ring finger (murF) genes. Antibiotic susceptibility testing of 51 staphylococcal isolates comprising 34 Staphylococcus aureus (S. aureus) and 17 coagulase negative staphylococci (CoNs) revealed a highest sensitivity against vancomycin (100%) and marked resistance patterns against β-lactam (beta-lactam) antibiotics. The results revealed that 97.1% of S. aureus isolates demonstrated a high level of MDR pattern, being resistant to more than 3 antibiotics of different classes. The in vitroantibacterial effects of clove and Nigella sativa essential oils against 11 MDR isolates using disc diffusion method indicated that both oils exhibited strong inhibitory efficiencies with inhibition zone diameters up to 45 and 20 mm, respectively. Besides, broth microdilution test of both essential oils revealed maximum activities against the tested strains with minimum inhibitory concentrations (MICs) up to 0.5 and 8 µg/mL for clove and N. sativa oils, respectively. Quantitative RT-PCR (real time polymerase chain reaction) analysis revealed the effective role of N. sativa and clove oils on the down-regulation of S. aureus murF and pbp < /em>2 genes. In conclusion, the above findings highlight the promising antibacterial functions of N. sativa and clove essential oils in the treatment of emergent resistant S. aureus infections.