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The present study examines the population genetic structure of fifty-nine specimens of Glis glis (Linneaus, 1766) from thirteen localities in central Europe, sequencing a 400-bp segment of the mitochondrial cytochrome b (cyt b) gene and a 673-bp segment of the cytochrome c oxidase subunit I (COI) gene. The consensus tree obtained from Bayesian analysis revealed a robust dichotomy, showing two sister groups: one clade includes samples from a wide geographical area, extending from north-central Europe to northern Italy (major branch sensu Bilton), and the other comprises samples collected in central and southern Italy and in Sicily (Italian branch). According to the Tajima-Nei model, the two phylogroups were separated by a sequence divergence of 0.8% (cyt b) - 2.6% (COI), showing the COI gene to be more informative than cyt b. On a smaller geographical scale, the Italian clade was further substructured, displaying geographical differentiation along the Peninsula. The gene pool in this area was patchy; whereas populations from Sicily Island demonstrated fixed cyt b and COI haplotypes, assuming processes of isolation and selection. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, , 11-21. [ABSTRACT FROM AUTHOR]