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In this study, genetic structure and pathogenic diversity of Sclerotinia sclerotiorum, the causal agent of white cottony stem rot, were assessed through Mycelial Compatibility Groupings (MCGs) and comparison of isolate virulence. 65 isolates from six different hosts from three northern provinces of Iran (Golestan, Mazandaran and Gilan) were placed at 39 different mycelial compatibility groups. The observed MCGs differed within three regions. From all MCGs, 61.53% and 15.38% belonged to Mazandaran and Golestan and 10.25% and 12.82% were common between Mazandaran and Gillan and Mazandaran and Golestan, respectively. Shannon diversity index (Ho) of MCGs for the whole regions was 1.509 (Htot). Partition of total diversity (Htot) showed that 68% corresponded to a variation in diversity within S. sclerotiorum populations. Study on virulence was tested using a stem inoculation technique under greenhouse conditions. Evaluating of severity by two methods Stem Lesion Length and the Area Under Disease Progress Curve (AUDPC) showed that isolate virulence varied within the foue clade. 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. [ABSTRACT FROM AUTHOR]