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As a result of human activities, natural Mediterranean landscapes (including agro-ecosystems) are characterised by a mosaic-like structure with habitat-patches at different successional stages. These systems have high biodiversity levels and are home to a large number of species protected by European laws whose habitats should be adequately managed. In the present work, we study habitat use from an applied point of view in the spur-thighed tortoise Testudo graeca, an endangered reptile present in semi-arid Mediterranean agro-ecosystems. Results show that, at a landscape scale, the species selects simplified vegetation structures and includes in its home range re-colonisation shrubland and small non-irrigated fields. Within the home range, habitat selection patterns vary and areas with higher vegetation cover and complexity are selected. Detected patterns are discussed in terms of the ecological requirements of the species and with a hierarchical view of resources and conditions. The implications of our findings for habitat management aimed at the conservation of the species are also discussed.