The effect of thyme oil (96 μL L−1) vapours on the expression of phenylalanine ammonia-lyase (PAL) and lipoxygenase (LOX) genes, and control of anthracnose was investigated in naturally infected ‘Hass’ and ‘Ryan’ avocado fruit stored for 21 d at 7–7.5 °C, and thereafter kept for 5 d at 20 °C, simulating the supply chain conditions. Exposure to thyme oil vapours prior to cold storage resulted in up-regulation of the PAL gene expression in both ‘Hass’ and ‘Ryan’ avocado when compared with untreated fruit and those treated with prochloraz®. The higher expression of PAL gene was observed in ‘Ryan’. Thyme oil vapours exposure resulted in the higher epicatechin content. At the same time, exposure to thyme oil vapours led to down-regulation of LOX gene expression in both cultivars. Thus, simultaneous up-regulation of PAL gene and down-regulation of LOX gene in avocados exposed to thyme oil vapours prior to cold storage was associated with higher epicatechin content in the fruit. Therefore, it can be concluded that postharvest application of thyme oil vapours increases anthracnose disease resistance in ‘Hass’ and ‘Ryan’ avocado fruit.