The onager Equus hemionus onager, a wild ass endemic to Iran, is categorized as Critically Endangered on the IUCN Red List. Its biology and conservation requirements are poorly documented. We report our observations, made in 1997 and 2000, on the behaviour and ecology of the two remaining populations, located in the Touran Protected Area and the Bahram-e-Goor Reserve. Recent population counts by the Department of Environment of Iran (471 in the Protected Area and 96 in the Reserve) are markedly lower than the estimate of 600–770 made in the 1970s in the Touran Protected Area. We observed social interactions between stallions and mares outside the breeding season that contrasts with the known social structure of this subspecies. Poaching, competition with domestic animals, removal of shrubs for domestic use, and land conversion have been identified as the main threats to the two remaining onager populations. In addition, geographical isolation could cause the loss of genetic variability in these two relatively small populations, and also makes them more susceptible to the potential effects of stochastic events such as drought or disease. Public awareness, appropriate protection, and scientific studies must be urgently supported by both national and international organizations in order to prevent the extinction of these two apparently dwindling populations of onager.