Myotis bechsteinii is a European forest bat species. It’s considered rare and only locally abundant over its wide distribution range. Current rareness- in strong contrast to the abundance in the fossil register- and its distribution restricted to large masses of well preserved deciduous forest, suggest that Myotis bechsteinii is retreating, as a consequence of climatic factors, deforestation or both. The comparative study we conducted does not support the vision of the Mediterranean area as suboptimal for the species, but rather the opposite. Thus, the reported scarcity of this bat in the area seems to be more related to degradation and rarefaction of preferred habitats- deciduous forests- than to bioclimatic conditionings. Genetic structure also reflects the prolonged isolation of populations, related to deforestation and to low altitude mountains acting as corridors promoting connectivity. Given the slow and limited responsiveness of Myotis bechsteinii to perturbations to their habitat or populations, the present distribution- smaller than the potential habitat- may reflect the history of fragmentation and degradation of forests, even at finer spatial scales.