Successful management of endangered species may be greatly facilitated by the ability to monitor population trends. The Australian northern hairy-nosed wombat (Lasiorhinus krefftii) is one of the world's most endangered mammals, but precise abundance estimation by trapping surveys has proven exceedingly difficult. A mark-recapture study was conducted in the sole remaining L. krefftii population, based on microsatellite identification of individuals and their gender from DNA in remotely collected single hairs. Population size was estimated to be 113 (95% confidence interval of 96 to 150). This suggests an increase in population size over the previous estimate of 65 (95% CI 42-186) in 1993, although the estimates did not differ significantly. There was a significant male bias in the sex ratio (2.25 males:1 female), in agreement with recent trapping surveys. The non-invasive approach used here is vital for estimating population size and trends, and hence it is the most important recent advance in the conservation management of the northern hairy-nosed wombat.