The advent of next-generation sequencing techniques has the potential to revolutionise our understanding of phylogeographic processes in mammals at a continental scale. Studies of mitochondrial DNA variation have revealed little structure in many carnivore species in Europe, despite their presence in different glacial refugia during the Last Glacial Maximum. To determine if next-generation sequencing techniques could uncover further levels of genomic structure in European carnivores, a total of 524 red foxes (Vulpes vulpes) stretching from Ireland in the west to Siberia in the east were genotyped using genotype-by-sequencing (GBS). Just over 15,000 ‘neutral’ SNPs were retained after various filtering steps and tests for outlier loci. We have identified seven clusters using individual-based Bayesian methods (fastSTRUCTURE), and six using a Discriminant Analysis of Principal Components (DAPC) at the population-level. These clusters correspond to known refugia in the Mediterranean peninsulas, as well as Scandinavian, Russian and the island populations (Ireland and Great Britain). Levels of genomic diversity were similar among populations but were generally lower in the island populations and in the most northerly populations in Scandinavia. Ongoing work will incorporate the use of Approximate Bayesian Computation (ABC) to simulate different re-colonisation scenarios, with an additional focus on adaptive processes in this charismatic carnivore across Europe.