In this research, the genetic peculiarities of the common partridge (Alectoris chukar) have been investigated using a non-invasive sampling method and microsatellite markers in six loci. During 2014 and 2015, one hundred feather samples have been collected from four northwestern provinces of Iran. Our findings indicated that in Ilam, Kermanshah, and Hersin, there are two distinct subpopulations that have been diverged from other populations (Fst = 0.1). The highest diversity was recorded among the Kordestan populations, which can be related to the traditional culture of target species relocation, releasing in different places by the locals. The highest allelic frequency of 13.15 (and effective allelic frequency of 20) was recorded in Marivan subpopulation, which can be related to winter sampling along with the species' narrow migration routes to a warmer region. Because of this, the later subpopulation also showed deviation from the Hardy-Wienberg equation as well. Finally, two stepwise and two steps mutation models didn’t indicate any historical bottleneck, then the species currently face no serious threats.