The tested isolates of S. sclerotiorum obtained from different localities of Upper Egypt were able to infect common bean Balady cv. causing Sclerotinia rot disease with different degrees of disease severities ranging from moderate to sever. Isolates consisted of eight vegetative compatible groups (VCGs); three of them consisted of two different isolates (3EB, 5EB), (3EB, 6ED) and (5EB, 6ED) and the remaining 5 VCGs each consist one isolate, compatible only with itself.  Cluster analysis of electrophoretic patterns of proteins obtained by PAGE and SDS-PAGE and isozyme obtained by PAGE were able to differentiate the tested isolates of the pathogen, according to similarity levels, to different groups, however, they unable to detect differences among isolates in DNA when RAPD-PCR was adopted using two primers