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The present study reveals the occurrence of high genetic diversity within three wild edible Lentinus species of Nagaland, India viz. Lentinus squarrosulus, L. sajor-caju and L. tigrinus which remain under-utilized. The uses of three different markers i.e., inter simple sequence repeats (ISSR), directed amplification of minisatellite DNA (DAMD) and RAPD) both individually and in combination in the present study provided a convenient method to study the genetic variation and diversity in the 18 accessions of the three Lentinus species. All the marker systems used were found to be highly efficient and informative in discriminating the mushroom species. The Unweighted Pair Group Method with Arithmetic Average (UPGMA) dendrogram also revealed the extent of genetic relationship among all the accessions of Lentinus species which was confirmed by principle coordinate analysis. Genetic variability and diversity assessment at intra- and inter- specific levels are vital for crop improvement because the presence of natural genetic variation is crucial to have opportunities for development of improved traits in crop production. This study throws light on the potential of mushrooms especially the edible mushrooms as an economically valuable crop. Understanding the genetic diversity of any crop plant including edible mushrooms will play a beneficial role in food security.