In this study, the effect of mycorrhiza on the antioxidative system of Satureja khuzistanica plantlet has been investigated to increase its compatibility on ex vitro conditions. The relative gene expression of PAL, total flavonoid rate, activity of PAL enzyme, antioxidative enzymes and the rate of membrane lipid peroxidation in micropropagated plantlet after inoculation were measured in four steps after being transferred to ex vitro conditions. The relative expression of PAL gene (biosynthesis gene of flavonoids) increased in the leaves and roots of AM plantlets compared with non-inoculated plantlet. Increasing the relative gene expression of PAL increased the biosynthesis of the PAL enzyme and subsequently flavonoids in AM plantlets which leads to the integrity of the membrane and inhibition of oxidative damage in transition stress conditions. The enhancement of antioxidant enzymes (catalase, peroxidase) in the non-inoculated plantlet indicates that the rate of oxidative stress in the control plantlet is higher than AM plantlet. The higher amount of the rate of membrane lipid peroxidation in non-inoculated plantlet showed that the transition stress has enhanced the peroxidation of lipids, therefor, AM is able to help the plantlet to exhibit more resistant to this stress. By increasing the gene expression of the biosynthetic pathway of the flavonoids, it reduces the oxidative stress on the tissue culture plants.