We investigated the origins and persistence of European pine marten (Martes martes) populations across the British Isles by identifying mitochondrial DNA (mtDNA) sequences from contemporary populations (sampled since 1981) and comparing these with those of older 'historical' museum specimens (pre-1981) originally collected from the same geographic areas. Excluding Scotland, where the haplotype composition of populations appears to be unchanged, haplotypes found in contemporary and historical marten populations elsewhere differed both temporally and geographically. While these data suggest that the contemporary Irish population is descended from a relict population that passed through an early to mid 1900s bottleneck, the historical and contemporary English and Welsh populations differ in their abundance of specific mtDNA control region haplotypes. These data appear to suggest that particular haplotypes may have been lost from England and Wales at some point in the early to mid 1900s, but further nuclear DNA work is required to determine whether this shift has occurred by rapid genetic drift in the mtDNA control region or whether relict populations have been replaced by pine martens from elsewhere. If the reported shifts in mtDNA haplotypes reflect population extirpation events, historical pine marten populations of England and Wales would appear to have become extinct in the twentieth century (in Wales after 1950 and in England after 1924). Additionally, the recent occurrence of haplotypes originating from continental Europe, and of M. americana, suggest that relict populations of England and Wales have been replaced by, or hybridised with, occasional released, escaped and/or translocated animals. The implications of these results for pine marten conservation, and particularly reintroduction, are discussed.