The question of how reindeer pastoralism came about has been the subject of recurrent scientific inquiry from many different disciplines. In order to investigate the genetic traces within a Fennoscandian transition from a predominantly hunting economy to reindeer pastoralism, we obtained sequences from the mitochondrial control region from 193 reindeer samples from several archaeological sites dated between 1000 and 1700 CE in Finnmark County, northern Norway. A comparison with similar data from more recent archaeological sites, including extant domestic reindeer, demonstrates that the mitochondrial genome in Finnmark reindeer has gone through massive genetic replacement since medieval times characterized by a significant loss of native mtDNA haplotypes, together with a significant introduction of new haplotypes. Out of a total number of 62 haplotypes identified in both the modern and archaeological samples, only 14 were detected among samples known to represent domestic reindeer, while nine of these haplotypes were completely absent from the more ancient sites. Our documentation of a major genetic shift during the 16th and 17th centuries suggests that non-native animals were introduced during this period, at the same time as the transition to reindeer pastoralism took place.