The aim of this research was to study the genetic structure of the Afghan Pika’s (Ochotona rufescens) populations in Northern Khorasan province in order to determine their isolation rate. A total of 122 samples from four sample groups (Ghorkhod, Golol-Sarani, Salouk and Sarigol) were selected and the genotypic features were detected using 7 microsatellite loci. The results showed that all of the loci were subject to polymorphism and the allele ranged from 2 – 7. Significant Fst and Rst values were found among the populations based on the AMOVA test. Based on the Assignment Test, more than 90 percent of the individuals of the populations belonged to their original population (only 10 percent of the individuals belonged to other populations). A Paired comparison of genetic differentiation between the populations revealed significant deferences among them. The results of the Prichard model grouping showed that the samples collected in this study were approximately 7 groups. The results of AMOVA analysis revealed a significant genetic structure among different populations. Also, the majority of the variance is related to the variance within the population. There seems to be a different but small genetic structure among the studied populations
