Nagaland is a state of India which lies in the northeast part of the Indian continent. The majority of the forest area of the state is still unexplored. Nagaland has rich biodiversity including wild mushrooms. There are many medicinal mushrooms available in Nagaland like Auricularia auricula-judae, A. polytricha, Lentinula edodes, Schizophyllum commune, Trametes gibbosa, T. versicolor, Pycnoporus cinnabarinus, Microporus xanthopus, Coprinus disseminatus, Daldinia concentrica, Ganoderma lucidum, Aleuria aurantia etc. Mushrooms are one of the most sought after food in Nagaland because of their nutritional and medicinal properties. This investigation is an attempt to study the phylogenetic relationship of the medicinal mushrooms using bioinformatics approaches. This study was based on the multiple sequence alignment of the nucleotide sequence of the mushrooms and generation of their phylogenetic tree to infer their evolutionary history.