Hypsizygus marmoreus is a mushroom with abundant flavor and medicinal properties. However, its application is limited by problems such as long cultivation period, low biological efficiency, and microbiological contamination; therefore, there is a substantial need for development of new cultivars of this species. In this study, 55 strains of H. marmoreus were subjected to inter simple sequence repeat (ISSR) analysis to identify markers for the selection of mother strains for breeding from the collected germplasm. ISSR 13 and 15 were confirmed as polymorphic markers. The three strains (KMCC03106, KMCC03107, and KMCC03108) with white cap color were found to be genetically closely related upon UPGMA analysis of both ISSR 13 and 15. Based on the PCR analysis results for ISSR 15, the collected germplasm were differentiated into three groups according to the strain collection year. Thus, ISSR 15 could be a marker for determining the phylogeny of cap color and genetic variations according to the strain collection year. These results suggest that ISSR markers can be effective tools for the selection of mother strains for breeding of H. marmoreus.

H. mamoreus is a mushroom with abundant favor and medicinal use. However, its cultivation has problems such as the long cultivation period, low biological efficiency and microbiological contamination, so new cultivars should be developed. In this study, 55 strains of H.marmoreus were analyzed with ISSR markers to identify precise genetic information in collected germplasm as mother strains in breeding. ISSR 13 and 15 markers were confirmed polymorphism. The three strains (KMC03106, KMC03107, and KMC03108) with white cap color were close genetic relationship in the UPGMA analysis of both the ISSR 13 and 15 markers. Especially in the PCR result of the ISSR 15, the collected germplasm were differentiated to three groups following collecting year. As these results, the ISSR 15 marker would be able to classify the phylogeny of cap color and genetic variation along the collecting year. Therefore ISSR markers will confer effective selection of mother strains for breeding of H. mamoreus.