In present study, genetic diversity and differentiation in passer domesticus populations sampled from northern and southern Zagros Regions was investigated using (TG)9A-ISSR and (TG)9C-ISSR markers. 89 samples were obtained from six subpopulations during June to September 2010. (TG)9A and (TG)9C primers amplified 30 and 22 fragments, respectively. Results indicated considerable genetic variation at the species level (percentage of polymorphic bands (PPB) = 90.0%; Shannon’s information index (I) = 0.383 and Nei’s genetic diversity = 0.234). The Maximum and minimum genetic distance was observed between Tashan and Gheshlagh Dam subpopulations from Sanandaj and Salamn Farsi and Asadabad subpopulations from Behabahan respectively. The mean coefficient of gene differentiation (Gst) was 0.045, indicating that 95.5% of the genetic diversity resided within the population. Analysis of molecular variance (AMOVA) indicated that 2% of the genetic diversity among the populations was attributed to the geographical location while 92% was attributed to variations within the individuals inside the populations. An overall value of mean estimated number of gene flow (Nm) was equal to 0.377.
