Whooper swans have two old and new populations, the new population has reported since 2007. The current study aimed to investigate the genetic structure of this species and compare their gene pool, especially the new population. For this purpose, 110 samples from Iran and four European countries were analyzed, using six microsatelite loci. In addition to the samples of the emerging population in Fereydoonkenar International Wetland and the old population of Gilan, samples from Iceland, Sweden, Finland and Poland were also examined. The observed average heterozygosity ranged from 0.598 to 1.0 and the expected heterozygosity ranged from 0.661 to 0.950. Iceland in the extreme west of Palearctic had the highest observed heterozygosity of 1.0 and Iran in the easternmost part of the study area had the highest effective allele frequency (12.72). Also, the population of Iran showed deviation from Hardy-Weinberg equilibrium, except for one loci. Based on the STRUCTURE 2.3.4 results, the Iranian swan population had the highest gene flow due to the high dispersion of breeding colonies in northern latitudes. Therefore, the autumn and winter migrant swans have two populations in Fereydunkanar and one separate population in Guilan. Generally, the high allelic richness in the new population indicates a high conservation value of  the Fereydoonkenar wintering colony.