Prior to human arrival in the 13th century, two large birds of prey formed the top of the food chain in New Zealand. In the absence of non-volante mammals, Haast's Eagle, the largest Eagle in the world, and Eyles' Harrier one of the largest Harrier in the world, had filled ecological niches that are elsewhere occupied by - for example - large cats or canines. Genetic evidence has identified Haast's Eagle as a close relative to the small Australian Little Eagle, but the phylogenetic relationships of Eyles' Harrier are unknown. Here we use mitochondrial genome data to show that, like Haast's Eagle, Eyles' Harrier is a close relative of a small Australian open land species and that both New Zealand island giants diverged from their small Australian relatives as recent as the Pleistocene. The study sheds light on the biogeographic and evolutionary history of New Zealand's prehistoric apex predators.