This paper aims to study the impact of microhabitats and seasonal variations on antioxidants components in Thymus capitatus plants growing in nature. T. capitatus is a perennial xerophyte growing naturally at calcareous hills and wadis closest to the Mediterranean region. Freshly terminal shoots of T. capitatus and associated soil were collected from Wadi Habis (west Matrouh), Egypt. The plant samples were studied from three microhabitats; upstream, wadi-runnel and wadi-bed during winter and summer, 2018. Soil physical analysis was done. In plant samples, water content, malondialdehyde (MDA), specific activities of peroxidase (POD), polyphenoloxidase (PPO) and phenylalanine ammonia lyase (PAL) and proline content, total phenols, anthocyanin, chlorophyll a, chlorophyll b, and carotenoids, were determined. The specific activity of PPO was increased in the summer season while water content increased in winter. The other parameters were not changed significantly by seasonal variations. Regarding microhabitats effect, MDA attained the highest value in those at upstream, proline content was found higher at wadi-runnel, while PPO, POD, PAL, chlorophyll a, chlorophyll b, carotenoids, anthocyanin and total phenols were the highest in those at wadi-bed. Our results indicated that T. capitatus is highly tolerant to drought stress via keeping stability on MDA content.