Most studies on habitat selection among animals are conducted at local scales, whereas reliable determination of species requirements at larger spatial scales can be problematic. We used data available for NATURA 2000 sites to determine the habitat requirements of two relatively widespread and common species-pine marten Martes martes and stone marten Martes foina-in Southern Europe. Using presence-absence data, we applied statistical models at two spatial scales. At the local scale (within the dispersal distances of the species), sites occupied by martens were compared with unoccupied sites using buffers of different sizes, whereas at the regional scale, unoccupied sites were selected randomly. To adjust for spatial autocorrelation of data, penalised quasi-likelihood approximations were used. Both species of martens demonstrated preferences for areas with higher proportions of forest cover and steeper terrain. At the local, but not at the regional, scale, pine martens occurred at lower elevations, whilst stone martens occurred at higher elevations. We found that climatic variables (mean temperature, precipitation) had no significant effect on the presence of the martens. The results of our analyses generally confirmed findings of previous studies on habitat selection of both marten species in Southern Europe. This demonstrates the utility of data collected for NATURA 2000 sites for use in various analyses such as conservation planning and evaluating the impact of climate change on the distribution of animal species.