Seventy - five isolates of the fungus Zymoseptoria tritici, collected from seven wheat producing provinces in Iran, were studied using the molecular markers ISSR and SSR to determine its structure and genetic variations within its populations. Results indicated that the populations of the causal agent of this disease had a relatively high level of genetic diversity, with the total average genetic diversity (Ht) of 0.34 in the studied samples. When the genetic diversity was divided by the genetic diversity within and between the tested fungal populations, intra - population and inter - population genetic diversities were, respectively, 69 and 31%. Moreover, results showed that there was a strong gene flow between the studied provinces. The maximum genetic diversity among the studied provinces was observed in Ardebil and Khuzestan Provinces, and cluster analysis also revealed that the fungal populations of these two provinces had the greatest similarity with each othe
