Historically, the onager or Persian wild ass Equus hemionus onager, endemic to Iran, was widespread on the arid and semi-arid central steppes but only two natural populations remain. We estimated the population density of the onager in Qatruiyeh National Park using line transect distance sampling. Transects were surveyed on three plains in the Park and the results compared with total counts conducted by the Department of Environment. Our estimate (109 onagers per 100 km2; 95% confidence interval 67–179) is similar to that obtained by the total counts (137 onagers per 100 km2). Distance sampling is therefore a promising method for estimating the abundance of the onager. Using the annual censuses performed by the Department of Environment over the last 13 years we estimated that the population has a growth rate of 0.09. During the same period the onager population in the Touran Protected Complex has experienced a severe decline. The high density of onagers within the National Park indicates the unsuitability of adjacent habitats, including Bahram-e-Goor Protected Area, for this species. Lack of sufficient security and poorly distributed water sources appear to be the main reasons discouraging onagers from entering the Bahram-e-Goor Protected Area. We recommend and describe management interventions that could potentially assist in maintaining the last surviving onager populations in Iran.