The Great Auk, Pinguinus impennis, was once found in large numbers across the North Atlantic. However, in June 1844 the last two individuals ever reliably seen were killed, and another species was lost forever. While the Great Auk’s extinction was probably caused by overhunting, it is not known whether its’ disappearance was facilitated by stress due to increasingly warm and less favourable habitats. Ancient DNA research provides a powerful tool that enables us to learn from the past and to evaluate and investigate factors that influence species’ extinction. This evolutionary time travel allows us to explore species’ response to environmental change by inferring population dynamics and correlating these with environmental changes. As one of few cold-adapted marine bird species in the Northern Hemisphere to have gone extinct in the Holocene, the Great Auk lends itself well to be a model species to investigate and understand extinction risk from environmental change, and therefore allow us to help endangered species of today. To investigate the relative importance of environmental change and human hunting in the extinction of the Great Auk, we used the latest ancient DNA extraction, capture enrichment and high-throughput sequencing techniques to sequence complete mitochondrial genomes from Auks from across their range. Interestingly, the results show significant genetic diversity and no evidence of phylogeographic structure or a recent bottleneck. This suggests that genetically diverse populations were migrating and mixing throughout their large range, a finding very much in contrast to expectations of a species under threat of extinction. This insight into the genetic history of the Great Auk only adds to the mystery of the bird and its demise and raises the question whether intensive hunting alone could have driven the species to extinction.