Petroleuciscus esfahani , a member of Cyprinidae family, widely distributed in Zayandehrud and Karoon River basins in Iran. Considering the importance of the genetic variation and population structure for management and conservation of species, especially native fish, the genetic diversity of Zayandehrud chu was investigated using molecular techniques in response to Cadmium pollution. In this study 30 specimens of Zayandehrud chub were collected from each locality (Khersoonak (KH), Cheshmeh Dimeh (CHD), Safaeieh bridge (S.B) and Chamgordan (CH) stations). Cadmium concentration in gill, muscle, kidney and intestine tissus were determed with atomic absorption spectrometry. For molecular study, DNA was extracted using Bio basic kit of Genet-Bio from bodies tissues collected from each stations. The DNA quality was examined by electrophoresis on 1% agaros gel and painted with ethidium bromide. PCR amplification was performed using five pairs of microsatellite primers (CtoF-172, BL1-2b, CnaB-030, LleA-071 and Ca3) at annealing temperature of 56-58 ° C. PCR products electrophoresed on 12% achrylamid gel and painted with silver nitrate. PowerMarker ver 3.0, PopGene ver 3.2, ARLEQUIN ver 3.11, MEGA ver 4 and NTSYS ver 2.02 softwares were using for data analysis. The level of Cadmium in muscles was the lowest while in kidney tissue was the highest, because of the aggregation and long preservation in tissue. Pollution concentration increase from upstream (KH and CHD) to down stream (S. bridge and CH) because of sewage of steel meel arrived to down stream. Number of the observed alleles at all station ranged from 9.6 (CHD) to 8.6 (3 other population) and number of effective alleles was from 6.84 (CHD) to 5.66 (CH). The mean of polymorphism information content (PIC) at all loci was 0.826. Among the five pair markers, CnaB-030 was the less polymorphic and Ca3 the most polymorphic one. The expected heterozygosity ranged from 0.82 in KH CH and 0.85 in CHD and averaged 0.849. The observed heterozygosity ranged from 0.92 in CH and 1.00 in KH and averaged 0.978. Significant deviations from Hardy–Weinberg Equilibrium expectation were found at CnaB-030 and Ctof-172 in all populations, BL1-2b in KH, CHD S.bridge, LleA-071 in KH S.bridge and Ca3 in CH population ( p 0001). The analysis of molecular variance (AMOVA) indicated that the percent of variance among populations and within individuals were 2.20 and 97.80, respectively. Only a small proportion (2.20%) of the variation was attributed to differences between the populations and most of the variation was attributed to differences within individuals. The overall value of F ST between populations was 0.025. The genetic similarity and distance index came in the range of 0.756-0.859 and 0.141-0.244, respectively. The level of genetic variability was high in the studied stations but comparison of mean expected heterozygosity values revealed that these loci did not show significant differences between the stations. There were existed significant differences in genetic variation among the stations and significant genetic differences was found between pairwise of stations, too ( p 005), that could be through Cadmium pollution, however existance of private alleles in all stations emphasis this subject, but this differences could not separate stations from each other. The low genetic differences between stations could be due to low geographic distance and high gene flow between stations. For better understanding of opulation structure of Zayandehrud chub in response to pollutions, population structure studies using other molecular techniques and other pollutions from all distributed areas followed by ecological and/or biological researches should be considered. Keywords : Zayandehrud chub; Petroleuciscus esfahani ; heavy metal; Cadmium; microsatellite; population variety; genetic differentiation.