Inter Simple Sequence Repeats (ISSR) and Sequence-Related Amplified Polymorphism (SRAP) markers were applied for genomic fingerprinting of 8 Hericium isolates of Turkey and American origin. The ISSR, SRAP and combined ISSR/SRAP analyses based dendrograms were generated by the UPGMA method. Fifteen ISSR primers amplified a total of 154 bands of which 151 (97.4%) were polymorphic, whereas 16 SRAP primer combinations amplified 164 bands of which 156 (95.1%) were polymorphic. All the Hericium isolates analyzed was divided into three major clusters and H. americanum independently located on the one cluster in all dendograms. The dendrograms indicated a clear pattern of clustering and the 8 Hericium isolates showed significant differences suggesting that they were far to each other in genetic relation. These results demonstrated that both methods were highly effective for discriminating among species and strains of Hericium. Finally, to our knowledge, this is the first application of ISSR and SRAP markers on the systematics of Hericium isolates and these findings would benefit future research in Hericium spp.