Until a few hundred years ago, New Zealand hosted several species of flightless ratite birds, collectively known as the moa. We have used mitochondrial sequence data for Dinornis, the largest of the moa, and new coalescent approaches to estimate its population size prior to human arrival ca. 1000-6000 years BP. We show that, as little as 1000 years ago, Dinornis numbered between 300,000 and 1.4 million and that the standing population of all moa species was ca. 3-12 million. This estimate is an order of magnitude larger than the accepted population estimate (ca. 159,000) for all moa species at the arrival of humans and suggests that moa numbers had already declined prior to human settlement.