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Population genetic structure of the Persian wild ass (Equus hemionus onager) was studied in Touran biosphere reserve and Bahram-e goor protected area using microsatellite markers. Due to high vulnerability of this endangered subspecies, collecting blood and tissue samples required for genetic study was impossible. Thus, fresh feaces and hair samples were collected because they were safe sampling methods. The microsatellite markers indicated that despite the habitat fragmentation and small population size, Touran and Bahram-e goor populations still belonged to a non-inbred panmictic population. However, discrepancy in their population growth rate over time might have affected and improved the genetic variation of the Bahram-eGoor compared to Touran population. Assessment of the variation in population size, over the past 88 to 111 years ago, did not show any abrupt reduction. Therefore, the genetic diversity of the Persian wild ass is still capable to cope with the natural disasters like drought. In conclusion, other factors such as poaching, habitat destruction and insecurity can be considered as the major causes of the reduction in population size of this endangered subspecies. [ABSTRACT FROM AUTHOR]