We address in this study the taxonomic status of the two major phylogenetic lineages of fat dormice, genus Glis . These lineages show unique mutations at 43 positions of the cytochrome b alignment and are classified as two distinct species, the European fat dormouse Glis glis (Linnaeus, C. . Systema naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis synonymis, locis, Vol. 1 . Laurentii Salvii, Holmiae [Stockholm]) and the Iranian fat dormouse Glis persicus (Erxleben, I.C.P. . Systema regni animalis per classes, ordines, genera, species, varietates cum synonymia et historia animalium. Classis I. Mammalia. Impensis Weygandianis, Lipsia [Leipzig]). The European dormouse is widespread in Europe, Asia Minor and the Caucasus, while the Iranian dormouse occupies the southern Caspian coast in Iran. Ranges are presumably delimited in Azerbaijan by rivers Kura and Aras. The two species differ categorically in size of the glans penis, size and shape of the baculum and in width of the posterior extension of the premaxilla. The Iranian fat dormouse has on average a more blackish distal half of the tail, a higher count for abdominal nipples, and a longer maxillary tooth-row. Intraspecific structuring in G. glis indicates a taxonomic complexity which is not yet understood and requires a comprehensive systematic revision. To define the nominal taxon objectively we designate voucher PMS 27369 (Slovenian Museum of Natural History) as the neotype for G. glis, therefore restricting the type locality for the species to Mt. Krim in Slovenia.