Bread wheat, Triticum aestivum L. is a major staple food for the world’s population. Cereal cyst nematode, Heterodera filipjevi is a soil-dwelling phytoparasitic nematode worldwide, which has a wider distribution than other species in Iran. The aim of this study was to search for a new source of resistance against the cereal cyst nematode, H. filipjevi in a collection of 43 irrigated and rainfed wheat accessions. Microsatellite markers, or simple sequence repeats (SSRs) were used to analyze the resistant and or susceptible wheat genotypes to H. filipjevi Isfahan pathotype populations. Seven primers were used, out of which five primers showed polymorphisms. Alleles per primer varied from 1-3 per locus (mean 2.85). The highest and lowest Polymorphic Information Content (PIC) of 0.81 and 0.44 (mean 0.66) were related to Xgwm 3012DL and Xgwm147, respectively. Genetic similarity was 29-88% between accessions. SSR analysis divided the accessions into five main groups. Resistant cultivars ‘Bam’ and ‘Behrang’ possessed both Cre1 and Cre8 resistant genes. The Cre3 and Cat genes were partially sequenced in five cultivars of different responses to H. filipjevi. The nucleotide sequences were compared to Cre3 and Cat homologues, indicating 93 to 100% and 86 to 92% homology, respectively. The MEGA program showed highest similarity of Cre3 and Cat genes amplified with the resistance gene analogues (RGA14) in the wheat and Cat3-A1 gene in ‘Carnamah’. This research showed that SRR markers could efficiently verify genetic diversity between wheat accessions, and the known resistance genes (Cre genes) against the cereal cyst nematodes could not control the H. filipjevi Isfahan pathotype populations, except with the Cre1 gene. The results on gene expression in the leaf indicated that the expression rate in the leaves of the plants treated with the H. filipjevi Isfahan pathotype was increasing with a high significant difference at 1% level. So that, the expression of the Cre3 gene in sixth and seventh weeks increased 8.88 and 9.77 times respectively. Whereas, in the case of TaPrx111 gene, it was 3.74 and 5.93 times in the sixth and seventh weeks, and with the TaPrx112 gene was 16.4 and 11.6 times respectively. The results of analysis of variance of gene expression in the root showed that, there was a significant difference between the accessions infected to H. filipjevi Isfahan pathotype and control. Expression of Cre3, TaPrx111 and TaPrx112 genes occurred by 32.6, 20 and 8.18 times four days after inoculation with the nematode in comparison to the control ones respectively. Whereas, seven days after inoculation the increase for each gene was 15.98, 5.93 and 16.59 times respectively. Also, the expression level in resistant cultivars was higher in the leaves and roots than in moderatly susceptibe and susceptibe cultivars significantly.