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The genetic structure of forest animal species may allow the spatial dynamics of the forests themselves to be tracked. Two scales of change are commonly discussed: changes in forest distribution during the Quaternary, due to glacial/interglacial cycles, and current fragmentation related to habitat destruction. However, anthropogenic changes in forest distribution may have started well before the Quaternary, causing fragmentation at an intermediate time scale that is seldom considered. To explore the relative role of these processes, the genetic structure of a forest species with narrow ecological preferences, the edible dormouse (Glis glis), was investigated in a set of samples covering a large part of its Palaearctic distribution. Strong and complex geographical structure was revealed from the use of microsatellite markers. This structure suggests that fragmentation occurred in several steps, progressively splitting the ancestral population into peripheral isolated ones. The fact that this structure postdates post-glacial recolonization, together with dating based on microsatellite data, supports the hypothesis that the differentiation was recent, starting around 9000 years ago, and took place stepwise, possibly up to Medieval times. This complements a classic phylogeographical interpretation based on the effect of past climate change, and supports the role of anthropogenic deforestation as a trigger of recent intraspecific differentiation.