It has been confirmed the association of oxalic acid with pathogenicity of Sclerotinia sclerotiorum isolates in the present study. The highly virulent SS 34 isolate of Sclerotinia sclerotiorum was found to be highly oxalic acid producer while the weakly virulent SS 2 isolate was poorly oxalic acid producer. The moderately virulent isolates, however, showed intermediate potential for oxalic acid production. These results were confirmed and explained at the molecular level analysis of Sclerotinia sclerotiorum isolates. The protein banding pattern based on the SDS-Page at 53-12 kDa showed ten bands for the highly virulent SS 34 isolate while only one protein band was recognized for the weakly virulent SS 2 isolate at this molecular weight. The moderately isolates however, showed intermediate number of bands of 3-6 bands at this protein range. Meantime, the highly virulent SS34 isolate showed unique protein bands at both53 kDa and 42 kDa, while, not any of the other analyzed isolates exhibited bands at this protein molecular weight. The only protein band recognized for the weakly virulent SS 2 isolate was at 24 kDa where all isolates showed protein bands at this molecular weight. Five primers were used to study the genetic variability between the tested isolates and the primer R3 showed enough potential to differentiate between the highly virulent and the weakly virulent isolates as nine bands were recognized with the highly virulent isolate while only four bands were existed for the weakly virulent one. The moderately virulent isolates, however, showed intermediate number of bands of 5-8 bands. Meantime, on the basis of the phylogenetic analysis and the constructed dendrogram based on the SDS-Page of the isolates protein and that based on the random amplified polymorphic DNA (RAPD), It was clear that the highly virulent Sclerotinia sclerotiorum SS 34 isolate and the weakly virulent SS 2 isolate were located in two distinct distant clusters. The moderately virulent S. sclerotiorum isolates, however, were located in intermediate sub-clusters.