Avian influenza is a contagious viral disease affecting the respiratory, digestive and nervous system of birds belong to orthomyxovirus family. In the chicken Mx gene, type of amino acid at position 631 determines the antiviral activity against influenza and vesicular stomatitis virus. A single nucleotide polymorphism (SNP) at position 2032, responsible for the variation of amino acid at position 631 (Ser to Asn) of the Mx protein, has been demonstrated to be responsible for positive or negative antiviral activity of Mx proteins., The allele A and G at position 2032 corresponds to the positive and negative antiviral activity, respectively. In order to identify gene polymorphism at Mx locus, 250 blood samples randomly were collected from Sari, Shiraz, Mashhad native fowls breeding station , commercial broiler and layer flocks. DNA was extracted and a fragment with the length of 299 bp from the exon 13 of Mx locus was amplified by a specific primer pairs. PCR-RFLP method was used to identify of polymorphism in coding sequence of the Mx gene using Hpy8I restriction enzyme. The frequency of alleles were estimated A (0.692) and G (0.308) in Sari, A (0.577) and G (0.423) in Shiraz, A (0.604) and G (0.396) in Mashhad, A (0.46) and G (0.54) in commercial broiler and A (0.86) and G (0.14) in layer strain, repectively. According to the observed polymorphism at position 631 of Mx protein and its important role in susceptibility to influenza disease it may be possible to use this marker gene in breeding programs.