For molecular evaluations of Fusarium graminearum, 76 isolates of fungi were collected from Mazandaran, Golestan and Ardabil provinces. DNAs were extracted from fungal isolates according to the method of Müller et al (1992). After assuring the quantity and quality of DNA, rep-PCR reactions were performed using BOX primer. Evaluations of genetic variation within each subgroup and for all isolates were achieved by POPGENE Version 1.31. Cluster analysis of isolates was performed with NTSYSpc-2.02e based on UPGMA method. The genetic diversity for the total population (Ht) was 0.336. The Shanen information Index and Gst were calculated to be equal to 0.4993 and 0.03 respectively. Genetic distance between sub-populations and within sub-populations was also calculated by POGGENE. Based on the Nei’s genetic distance and the UPGMA, a dendrogram was achieved between different sub-populations that was visible with TREEVIEW v.1.6.6. The genetic similarity between the two sub-populations of Mazandaran and Golestan was the highest (0.9882) and between the two sub-populations of Golestan and Ardebil (0.9675) was the lowest. Molecular evaluations showed that 76 different genotypes of Fusarium graminearum were present in the population. In dendrogram obtained from cluster analysis, 7 clusters and 2 sub clusters were achieved. With the exception of the cluster II, which includes mainly corn isolates, and the cluster IV, which described the geographical separation of some isolates to some extent, in other clusters of dendrograms derived from cluster analysis, the genetic isolation of isolates in these groups, was independent of geographical separation and also, their host specificity. Therefore, the isolates of the fungus have some genetic similarities which made them put together in a group apart from their host specificity and their geographical regions.