Ancient DNA (aDNA) was isolated from the bones of 290 individuals and four species of extinct New Zealand moa. All sampled bones had been recovered from a small geographic area (~10 km radius) near Waikari in North Canterbury. A total of 217 specimens were 14C-AMS dated, providing a temporal framework for the genetic analyses and an unprecedented opportunity to study extinct megafauna at the population level. Taxon and sex were determined for each individual, using aDNA technology. This revealed a large excess of females (overall ♂:♀ = 1:5.1), and significant compositional differences for the moa assemblages between fossil sites. Balanced sex ratios were observed among juvenile moa, suggesting that a gender-bias developed as the birds matured, probably as a result of higher male mortality. Female territoriality and ecological niche-separation are discussed in this context. Mitochondrial DNA (mtDNA), amplified using a quantitative PCR procedure, provided a measure of DNA preservation in each radiocarbon-dated fossil. This assessment showed that DNA degrades over thousands of years according to an exponential decay model, and the average molecular half-life for the here targeted DNA fragment was estimated to be 521 years. By using high-throughput sequencing, six polymorphic moa microsatellite markers were identified and characterised. These are the first microsatellite primers developed exclusively for extinct taxa. A high-resolution genetic study of the four sympatric moa populations was carried out, combining information from mtDNA, microsatellites, sex-identification, and radiocarbon age. Genetic diversity, past demography, kinship, and other aspects of moa biology were analysed. The populations showed a remarkable extent of genetic stability throughout the 3000-4000 years preceding their extinction, suggesting that they were large and viable before suddenly disappearing. The results represent significant advances in aDNA research and thanks to the high resolution in microsatellite markers, moa have here been studied, almost as if they were still alive.