Quercus species may be the most characteristic plants of the Mediterranean forest, and due to their economic and forestry interests, this study seeks to establish parameters indicative of environmental stress in two Mediterranean species of the genus Quercus, Q. suber and Q. ilex subsp. Ballota. Six sampling areas were located in protected zones of southern Spain. Among the indicators studied, we include malondialdehyde (MDA), hydrogen peroxide (H₂O₂) and other molecules that form part of the non-enzymatic antioxidant systems in plants, such as phenolic compounds, ascorbate, or proline. Our results show that the content in MDA, H₂O₂, phenolic compounds, and ascorbate were optimal indicators of environmental stress for both species. These results were different depending on sampling area. The present work therefore suggests that stress indicators could be a quick and effective tool for determining the ecophysiological behaviour of different Quercus species.