The variation within a population of 100 pieces of native chicken from 5 regions of Khuzestan province (Abadan, Dezful, Shushtar, Ahvaz, Izeh) were analyzed by using 6 microsatellite markers, in the present study. The DNA was extracted by using Salting Out method from blood samples collected. The PCR reactions for all locuses were performed and it was found that all of them are highly polymorphic.The frequency of studied locuses was obtained from 0.247 to 0.005.A total of 103 alleles were detected. The average of PIC rate was estimated (0.898). Average hetero-zygosity in whole population (0.948) detected Abadan, with the most level (0.97), and Shushtar with the lowest one (0.92). So Abadan and Shushtar have shown the highest and lowest levels, respectively.The Phylogenetic tree resulted from DA genetic distance was drawn by UPGMA method, that Shushtar known as the oldest population. The High level of genetic variation identified in this study, generally.
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