Nagaland has a rich macro fungal flora but not many works has been carried out till today. Present investigation deals with molecular characterization and phylogenetic analysis of six popular wild edible mushrooms (WEMs) species of Nagaland, India viz., Lentinula edodes, Lentinus squarrosulus, L. sajor-caju, L. tigrinus, Schizophyllum commune, Termitomyces heimii and one variety of L. squarrosulus based on molecular markers (ITS, 18S rRNA and 28S rRNA genes) data. The use of DNA markers for identification of mushrooms is highly desirable and practical because it is reliable and quick. This approach could resolve successfully the identity and interrelationship of six WEM species with respect to their infrageneric groups. The high CI values of the mushrooms species indicated the low homoplasy nature. The ITS and 28S rRNA data sets were found to be more informative then the 18S rRNA datasets. The molecular data generated for each mushroom species in the present investigation will help in correct identification and conservation of these widely consumed WEM of the region. Additionally assessment of bioactive molecules indicates that studied species are rich in pro-health bioactive compounds. The study hence throws light on the potential and importance of mushrooms especially the edible mushrooms as an economically valuable crop. [ABSTRACT FROM AUTHOR]