The aim of this study was to increase the Random Amplified Polymorphic DNA (RAPD) reproducibility by standardization of RAPD bands before 0 and 1 score and study of genetic variation of the Iranian Sclerotinia sclerotiorum isolates, which collected from Canola plant's fields. For this aim, twelve isolates are provided from different province of Iran which contains various growth degrees on Potato Dextrose Agar (PDA). The CTAB method used for genomic DNA extraction from Sclerotia powdered. The RAPD studied by 18 random primers. By using of three random primers (Ar0R2, Ar081 and Ar173) in arbitrarily primed (AP-) PCR a total of 284 RAPD products were compared in a sample of 12 individuals which contain highly polymorphism. Cluster analysis for PCR products of these three primers performed by UPGMA (Unweighted pair grouped method by arithmetic average) method. We found that RAPD profiles markedly differed between S. sclerotiorum isolates. Therefore, it is recommend that if the polymorphism of the isolates bands were standardized by migration of marker bands, RAPD technique not only could separate the isolates in multiple groups but also is an effective, rapid, reliable technique to study genetic variability between fungal isolates. Moreover, standardization RAPD polymorphic bands were used in the similar molecular techniques. RAPD markers may be a useful tool for investigation of the genetic variation within S. sclerotiorum isolates but these genetic variations were not significantly related with geographical positions of isolates
