Eudyptes spp. represents a species complex of crested penguins inhabiting the temperate and sub-Antarctic regions of the Southern Ocean. Current conservation efforts, however, are hampered by limited systematic and taxonomic understanding of this species-rich genus. Moreover, undescribed sub-fossil material from the New Zealand Chatham Islands and mainland New Zealand suggests at least one species of crested penguin may have become extinct during the recent Holocene. Several studies have used genetic evidence to describe species-turnover events in recent New Zealand history, including those extinction-replacement of yellow-eyed penguins (Megadyptes) and little blue penguins (Eudyptula). We hypothesise that a similar pattern may have been observed in New Zealand crested penguins. This study uses ancient and modern DNA (whole mitochondrial genomes and cytochrome oxidase 1) to (a) assess the systematic and evolutionary relationships between modern and extinct crested penguins, and (b) to explore the prehistorical distribution of Eudyptes taxa across the New Zealand region. An understanding of temporal shifts in crested penguin diversity is essential for prioritising conservation management strategies for these iconic taxa.