This study aimed to compare thyme, cumin extracts, and their nanoemulsion as antibacterial on S.aureus. The methods include , preparation of aqueous, oil extract and nanoemulsion from thyme and cumin, determination of MIC using the resazurin microdilution method, detection of mecA and coagulase genes by PCR before and after the treatment with nanoemulsions, figuring the bacteria after treatment using TEM. the result showed that the MIC values of thymus oil 100% , thymus oil nano emulsion 20% , cumin oil 100% ,cumin oil nanoemulsion 20% ,mix oil 20% ,thymus oil 20% ,cumin oil 20% ( 0.048, 0.156 , 1.562 ,10 , 0.625 , 0.312 , 10 ,) mg/m respectively , mecA and coagulase genes was absent after the in vitro treatment and TEM microscope showed the bacteria with extensive damage to the cell membrane. the result showed that nanoemulsion has a higher effect on S. aureus than essential oil alone