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Abstract: Aims: Enterohaemorrhagic Escherichia coli serotype O157:H7 as a major human pathogen is responsible for food borne outbreaks, bloody diarrhoea, haemorrhagic colitis and haemolytic uraemic syndrome and even death. In this study, the antibacterial activity of the Zataria multiflora essential oil (ZMEO) and nanoliposome‐encapsulated ZMEO was evaluated on the pathogenicity of E. coli O157:H7. Methods and Results: The minimum inhibitory concentrations (MIC) of essential oil (EO) were determined against the bacterium before and after encapsulation into nanoliposome. Then, the effect of subinhibitory concentrations was evaluated on Shiga toxin 2 (Stx2) production. The effect of free and nanoliposomal EO was also studied on the gene expression of Stx2 by real‐time PCR. It was found that inhibitory activity of EO was improved after incorporation into nanoliposomes (P < 0·05). The MIC of free EO against E. coli O157:H7 was 0·03% (v/v), while this value decreased to 0·015%, after encapsulation of EO into nanoliposomes. Furthermore, subinhibitory concentrations of liposomal EO (50 and 75% MIC) had significantly higher inhibitory effect on Stx2 titre than its free form (P < 0·05). Sub‐MICs of nanoencapsulated EO also showed a better activity in reduction of Stx2A gene expression than free EO. Using 75% MIC of nanoliposomal EO, the relative transcriptional level of Stx2A gene was decreased from 0·721 to 0·646. Conclusions: The findings of present study suggest that application of nanoliposomes can improve the antibacterial effect of EOs like ZMEO. Significance and Impact of the Study: Due to the enhancement of antimicrobial activity, nanoencapsulation of plant EOs and extracts may increase their commercial application not only in food area but also in the pharmaceutics, cosmetics and health products. [ABSTRACT FROM AUTHOR]