The role of southern European peninsulas as glacial refugia for temperate species has been widely established, but the role of cryptic northern refugia has only recently been addressed. Here, we describe the phylogeographic pattern of the forest-dwelling European pine marten (Martes martes), using a 1600-bp mitochondrial DNA (mtDNA) fragment from 287 individuals sampled across the entire distribution range of the species. To clarify the relationships between M. martes and its sister species the sable (Martes zibellina) in Fennoscandia and Russia, ten M. zibellina samples were also included in the analyses. Our results reveal the presence of 69 different haplotypes for M. martes and ten haplotypes for M. zibellina, which are split into three major assemblages: Mediterranean, central–northern European, and Fennoscandian–Russian clades, showing a global pattern of spatial segregation, with some area of overlap and genetic admixture. It is apparent that the Mediterranean phylogroup did not significantly contribute to the postglacial recolonization of most of the Palaearctic range of the species. Instead, most of Europe was colonized by the central–northern European phylogroup, which probably survived the last glaciations in northern cryptic refugia, as has previously been suggested by palaeontological studies. A highly divergent phylogroup has been discovered in Fennoscandia–Russia, which includes specimens from both Martes species. Calculations of divergence times suggest that the phylogroups split during the Pleistocene. Overall, our study indicates a complex phylogeographic history for M. martes, indicating a mixed pattern of recolonization of northern Europe from both Mediterranean and non-Mediterranean refugia, providing new insights into the existence of cryptic northern glacial refugia for temperate species in Europe. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 1–18.