The current spatial distribution of genetic lineages across a region should reflect the complex interplay of both historical and contemporary processes. Postglacial expansion and recolonization in the distant past, in combination with more recent events with anthropogenic effects such as habitat fragmentation and overexploitation, can help shape the pattern of genetic structure observed in contemporary populations. In this study, we characterize the spatial distribution of mtDNA lineages for fisher (Martes pennanti) in north-eastern North America. The history of fishers in this region is well understood and thus provides an opportunity to interpret patterns of genetic structure in the light of known historical (e.g. recolonization from glacial refugia) and contemporary events (e.g. reintroductions, fragmentation and natural recolonization). Our results indicate that fishers likely recolonized north-eastern North America from a single Pleistocene refugium. Three genetically distinct remnant populations persisted through the population declines of the 1800s and served as sources for multiple reintroductions and natural recolonizations that have restored the fisher throughout north-eastern North America. However, the spatial genetic structure of genetic lineages across the region still reflects the three remnant populations.