Aims The present study was conducted to investigate the effects of Thymus daenensis and Satureja hortensis essential oils (EOs) on the planktonic growth, biofilm formation and quorum sensing (QS) of some Staphylococcus aureus isolates (strong biofilm producers). Methods and Results Minimum inhibitory concentration (MIC) of the EOs, inhibition of biofilm formation as well as disruption of preformed Staph. aureus biofilms were assessed. The antibiofilm activity of the EOs was determined using microtitre plate test (MtP) and scanning electron microscope (SEM). The QS inhibitory activity was also examined on the pregrown biofilms by gene expression analysis using quantitative real-time RT-polymerase chain reaction (PCR) of hld gene (RNAIII transcript). Moreover, tetrazolium-based colorimetric assay (MTT) was performed to detect cytotoxic effects of these EOs on the Vero cell line. Finally, the major components of the tested EOs were determined using Gas Chromatography-Mass Spectrometry (GC-MS). The MICs of T. daenensis and S. hortensis EOs against planktonic cells of the isolates were 0·0625 and 0·125 μl ml−1 respectively. The minimum bactericidal concentrations for both of the EOs was 0·125 μl ml−1. The MtP test showed a significant inhibitory effect of the EOs on the biofilm formation and disruption at sub-MIC concentrations. These results were confirmed by SEM. Real-time PCR revealed a significant down-regulation of hld gene following treatment with MIC/2 concentration of S. hortensis EO. GC-MS analysis showed that carvacrol, terpinene and thymol were the major components of the applied EOs. Conclusions As selected EOs did not show significant cytotoxic effects even up to tenfold of MIC concentration, the applied EOs seem to be good candidates for preventing of biofilm formation of Staph. aureus cells.