Genetic structure and pathogenic diversity of Sclerotinia sclerotiorum, the causal agent of canola white stem rot, were assessed through Mycalial Compatibility Groupings (MCGs), a comparison and comparing of isolate virulence. Fifty-seven isolates from three different regions in Golestan Province were selected for mycelial compatibility and as well for virulence tests. Within the 57 tested isolates, 35 MCGs were identified, 42.86% of which being constituted of single isolate specimens, were all collected from Ali Abad region. The observed MCGs differed within the three regions. From among the 35 MCGs, 25.71%, 28.57% and 45.72% belonged to Kalaleh, Hashem Abad and Ali Abad, respectively. In Kalaleh, nine MCGs were identified all of which fell into two isolates. Ten MCGs were identified within the Hashem Abad region, eight of which represented two isolates and the remaining were constituted from three isolates. Sixteen MCGs were detected in Ali Abad for which, except one MCG which was constituted of two isolates, the rest belonged to one isolate. Moreover, no MCG was identified as common among these regions. Shannon diversity index (Ho) of MCGs for the whole regions found to be was 0.86 (Htot). Partition of total diversity (Htot) showed that 95.45% corresponded to a variation in diversity within S. sclerotiorum populations. Variation in isolate virulence was tested using a petiole inoculation technique under greenhouse conditions. Isolate virulence varied within the three regions. Moreover, in most cases the differences in virulence of isolates within MCGs were significant. The data indicated that populations of S. sclerotiorum obtained from the studied regions were composed of a heterogeneous mix of MCGs, therefore the population structure of this pathogen as well as variations in virulence of isolates must be considered in disease management systems in these regions.