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This work represents the first attempt to model the habitat-species relationships of a species of terrestrial tortoise on a large scale. We applied hierarchical variance partition methodology to Generalised Lineal Models (GLMs), with the presence of the tortoise in 1 km2 cells as the response variable. We posited the existence of a hierarchical scheme of factors (including climate, relief and lithology, and land-use) that determine the distribution of Testugo graeca in southeastern Spain. We also identified the environmental variables within each factor with the greatest explanatory power and decoupled local vs landscape effects. Climate, followed by relief and lithology, and then land-use, turned out to be the most important factor shaping the distribution of T. graeca in south-east Spain as well as determining the presence of the species within its range. Univariate models showed that the main climate constraints were related to rainfall and extreme minimum temperatures, two factors which could be related to constraints imposed by the length of the annual activity period and productivity. Finally, multi-scale decomposition suggested that neighbouring habitat and local dynamics may also be important in the distribution of the species at the landscape scale.