The great auk, (Pinguinus impennis), was a flightless bird, once abundant and widely distributed across the North Atlantic. It was, however, heavily exploited for its eggs, meat, oil and feathers, and latterly as a display item. Despite wide scientific and general interest in the species, it remains unclear if hunting alone was responsible for its demise, or whether it was already in decline due to other factors such as climate-driven environmental change. Here, we address various issues relating to the great auks’ evolution and extinction, including morphometric differentiation and population genetics. In contrast to previous findings, morphometric studies on humerus samples indicated no-significant population-specific size variation. High-throughput sequencing of ancient DNA (aDNA) samples of complete mitochondrial genomes from 41 great auks was undertaken from samples across the Holocene and Late Pleistocene range. Data showed consistently significant high levels of genetic diversity and gene flow persisting through time and across their range. Demographic reconstructions revealed the great auk had a large and stable effective population size, with no evidence of decline, associated with periods of climatic change. Population viability analysis indicated that harvesting of 5-7% of the total population would be required to cause extinction in a period of fewer than 350 years; levels commensurate with documented observations. Findings are consistent with the current consensus that human hunting was the primary cause of the great auks’ extinction. Additional analysis of nuclear DNA yielded no data due to low coverage of the 495 targeted markers. Related analyses on mitochondrial genomes of five candidate specimens and the organs from the last documented pair of great auks allowed for a 170-year-old mystery to be solved, by matching the male organs with the skin currently on display at the RBINS, Brussels. Collectively, our findings yield insights into the lives of an iconic extinct bird.