Investigating the evolutionary history of the species is critical for understanding the evolution of biodiversity and for its conservation. Towards this goal, molecular approaches are becoming increasingly powerful with the incorporation of recent theoretical and analytical advances. Here, we apply an isolation-with-migration coalescent-based model to control region and cytochrome b mitochondrial sequences to investigate the evolutionary history of European (Arvicola terrestris) and Southern (Arvicola sapidus) water voles throughout Eurasia. We date the time of the split of the common ancestor of European and Southern water voles around the fourth Mindel glacial (c. 252 000 bp), a date similar to that estimated by classical phylogenetic methods (c. 241 000 bp). Although postglacial expansions brought these species into secondary contact in Iberia and France, our results do not contain evidence of subsequent mitochondrial gene flow between descendant groups or current hybridization. We also estimate the effective population sizes of A. sapidus and Arvicola terrestris scherman on c. 199 000 and 52 000 individuals, respectively. This study illustrates the utility of modern coalescent-based genetic tools to investigate recent species and population divergences and sheds some light on the evolution of the genus Arvicola in Eurasia.