Wheat, Triticum aestivum L., is an important and strategic plant in the world, which is now due to climate change in the Iran, it is suffering from several diseases, including common root and crown rot. Therefore, a survey conducted during the growing season of 94-95 from the wheat fields of Isfahan Province and infected wheat samples to common root rot were collected from different regions and transferred to labs in nylon bags. Out of which, 48 isolates belonging to Bipolaris sorokiniana species were isolated and identified. The pathogenicity of the isolates was confirmed by selection of 10 isolates at random in laboratory conditions and inoculation of wheat seedlings, Parsi cultivar under greenhouse conditions. For phylogenetic studies, three isolates (B4, P1 and P5) were selected from the isolates for genomic DNA extraction and reproduction of the nucleus ITS region. To ensure the integrity of the sequences derived from each isolate, each sequence was compared with the sequences in the Gene Bank (NCBI) using the BLAST (Biological Local Alignment Search Tool). 72 isolates were selected from the gene bank. The sequences were matched with MEGA 7.0 software (Molecular Evolutionary Genetics Analysis, v 7.0). To evaluate the genetic diversity of the pathogenic fungal isolates, DNA extraction from 2 primer pairs of SSR including primer 1 (URP-1F, URP-2F) and primer 2 (URP-2R, URP-4R) was used to amplify PCR products. The results showed that the morphology and phylogeny of the fungus B. sorokiniana is the causal agent of the wheat root rot disease. In total, the corresponding primers produced 209 multi-shaped strips. The URP-2F and URP-4R primer pairs showed the highest polymorphic information content (PIC), H index (H), and Shannon index (I). The mean of PIC, H and I for total primers was calculated to be 0.89, 0.16, and 0.28, respectively. Cluster analysis carried out with NTSYS software by UPGMA method and Jaccard similarity matrix formulation that their cophentic coefficient was 87 percent. The results of this study showed that the SSR marker is a reliable marker system for detecting a high level of polymorphism for the genetic variability of B. sorokiniana isolates.