Molecular studies support the hypothesis that Corsica Island was a glacial refugium for a number of forest birds during the Pleistocene. We focused on the Corsican nuthatch (Sitta whiteheadi), an endemic passerine strongly associated with the laricio pine (Pinus nigra laricio). The range of laricio pine has been impacted by the Pleistocene glacial periods and forest has been recently fragmented by cutting and fires. Using both molecular (mitochondrial and nuclear) and morphological characters, we assessed the variation within the nuthatch population. Our results are consistent with the hypothesis that the Corsican nuthatch endured through the late Pleistocene and Holocene climatic variations, and sustained the subsequent cycles of forests reduction/expansion. The results also suggest that the recent anthropization of the landscape resulted in the isolation of a cluster of populations in the northern part of the island. The fragmentation of the habitat of the nuthatch may impede the future of the bird by creating isolated population units between which the gene flow is reduced.