Elucidating the colonization processes associated with Quaternary climatic cycles is important in order to understand the distribution of biodiversity and the evolutionary potential of temperate plant and animal species. In Europe, general evolutionary scenarios have been defined from genetic evidence. Recently, these scenarios have been challenged with genetic as well as fossil data. The origins of the modern distributions of most temperate plant and animal species could predate the Last Glacial Maximum. The glacial survival of such populations may have occurred in either southern (Mediterranean regions) and/or northern (Carpathians) refugia. Here, a phylogeographic analysis of a widespread European small mammal (Microtus arvalis) is conducted with a multidisciplinary approach. Genetic, fossil and ecological traits are used to assess the evolutionary history of this vole. Regardless of whether the European distribution of the five previously identified evolutionary lineages is corroborated, this combined analysis brings to light several colonization processes of M. arvalis. The species' dispersal was relatively gradual with glacial survival in small favourable habitats in Western Europe (from Germany to Spain) while in the rest of Europe, because of periglacial conditions, dispersal was less regular with bottleneck events followed by postglacial expansions. Our study demonstrates that the evolutionary history of European temperate small mammals is indeed much more complex than previously suggested. Species can experience heterogeneous evolutionary histories over their geographic range. Multidisciplinary approaches should therefore be preferentially chosen in prospective studies, the better to understand the impact of climatic change on past and present biodiversity.