In the present study, the polymorphism of myostatin gene (MSTN) in native chickens of Western Azerbaijan Rearing and Breeding Institute was investigated. The blood samples were collected from eighty two randomly selected hens. Genomic DNA was extracted from blood samples and a fragment of myostatin including 599 bp in promoter and exon 1 was amplified using PCR method. Breeding values for body weight and carcass traits were predicted by univariate animal mixed model analysis, using WOMBAT software. The effects of different SSCP genotypes on breeding and phenotypic values of the studied traits were evaluated by general linear model analysis. Three different single strand conformational polymorphism (SSCP) genotypes as AA, AB and AC were identified, with frequencies of 0.244, 0.549 and 0.207, respectively. Shannon and Nei gene diversity indices and number of effective alleles in the studied population were 0.88, 0.53 and 2.2, respectively, which indicated a high diversity of the studied population. Moreover, the studied population was not in Hardy-Weinberg equilibrium. The effect of the SSCP genotypes on breeding and phenotypic values was significant only in the case of breeding value for body weight at 12 weeks of age, whereas, the AC genotype individuals, significantly (P<0.05) had the lowest breeding value for body weight at 12 weeks of age. Based on the results obtained, it could be concluded that the studied fragment of myostatin gene is polymorphic in native chickens of Azerbaijan and could be used for marker assisted selection.