Several population studies of Sclerotinia sclerotiorum have been conducted and resulted in important publications furthering our knowledge of this pathogen. Microsatellite genotype data from those studies has been published with the notion that this data could be re-used by other scientists. However, amplicon sizes are known to vary across labs due to primer modifications for fluorophore labeling and the instrument used for fragment analysis. Thus, it is necessary to create a reference panel of DNA that represents allele sizes known to be present within the population. Given recent completion of genotyping of more than 366 S. sclerotiorumisolates from across the U.S., development of a DNA reference panel that represents most is now possible. Here, we identified 22 S. sclerotiorumisolates that were collected and genotyped previously and represented all known possible alleles. These 22 isolates were genotyped at 11 loci using two different methods. Results showed that seven of the 11 loci were reliable in generation of amplicon sizes, which allowed standardization of the genotypes generated in each method. The next step will be to identify additional published microsatellite loci used for S. sclerotiorum, to create a comprehensive reference panel that provides standards for all microsatellite loci genotyped to date. Taken together, the present results suggest that this method of creating a DNA reference panel will be an effective method to allow integration of previously published population genetic data of this plant pathogen.