Five species of CCNs, namely Heterodera avenae type B, H. filipjevi, H. hordecalis, H. latipons and Heterodera sp. 1 were reported from cereal fields and grasslands in Iran. Among these species, H. filipjevi most widely distributed followed by H. latipons and H. avenae type B. Based on previous surveys, H. filipjevi was found in Isfahan and Chahar Mahal va Bakhtiari provinces as the only species of cereal cyst nematodes. In Isfahan province 56.4% of soil samples were contained H. filipjevi with an average population of 6.02 eggs and J2/g of soil and in Chahar Mahal va Bakhtiari province, 42% of soil samples were infested to mentioned species with an average of 994 eggs and J2 per 200g of soil. This study was conducted to compare and determine the phylogenetic relationships of Heterodera filipjevi populations in wheat fields of Isfahan and Chahar Mahal va Bakhtiari provinces. The ITS-rDNA region of two populations belonged to Isfahan province and one belonged to Chahar Mahal va Bakhtiari province was amplified by TW81 and AB28 as forward and revers primers respectively. The PCR products were digested by restriction enzymes Hinf I, Rsa I and Pst I. A Comparison of the ITS-rDNA sequences of Isfahan and Chahar Mahal va Bakhtiari populations indicated approximately 99% similarity with those of the Iranian H. filipjevi and other countries in NCBI. The phylogenetic relationships among the populations were determined using Bayesian method. Analysis also showed low genetic distance between three populations of mentioned provinces in this study and the other Iranian populations (JX024208 and AF498380).