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.