Tan spot disease of wheat with the causal agent of Pyrenophora tritici-repentis is a very serious  disease throughout the world causing severe yield losses. Out of 163 isolates of the pathogen, collected from Golestan and Mazandaran provinces, 58 were selected for a study of population genetic structure. Selecting the real representatives from the whole population was carried out according to the results of the rep-PCR with BOX primers, and as well the locations of the isolates and the fields where the isolates had been collected. Population genetic structure of the pathogen was evaluated using rep-PCR as a molecular marker with three primers namely BOX, ERIC and REP. Three softwares of POPGENE, NTSYS-pc and GenALEx6 were utilized for data analysis. Population structure study among six sub-populations of the Iranian isolates revealed that 73% of the total variance was related to the variations within sub-populations while 27% of that related to the variance among sub populations. Mean gene diversity of the population was estimated as 0.3147. A dendrogram, based upon genetic similarity with Dice coefficient and UPGMA method showed no clear separations among isolates belonging to different races 1 and 2, so racial distribution of isolates is not found consistent with rep-PCR classification of the isolates in the dendrogram. There exists some consistency between geographical origin of the isolates and their genetic similarity. This is the first study covering population genetic structure of P. tritici-repentis in Iran. An evaluation of telemorph production regarding the pathogen, showed that pseudothecia (with asci and ascospores) were produced for 54% of the isolates while 17% of the isolates produced pseudothecia without asici and 29% while produced no sexual structures. It seems that beside the MAT gene and some other independent genetic factors, some macronutrients as well as humidity effect telemorph production.