Schizophyllum commune Fr. is valued for its high nutritional composition and medicinal importance. However, quality standards of this species have not been reported till date. The aim of the present study was to provide quality control standardization of S. commune based on organoleptic, microscopic, physico-chemical, chromatographic, molecular features and to partially screen its antioxidant activity. Physico-chemical parameters such as percentage of loss on drying, total ash, swelling capacity, water holding capacity, water solubility index and methanol extractive value were documented. In addition, fluorescence analysis of the powder using 16 different chemical reagents were carried out which exhibit a remarkable variation of colour against treating agents. Quantification of the major bioactive compounds present in the extract showed the following order phenol > flavonoid > ascorbic acid > β-carotene > lycopene. The antioxidant potentials of the extract were determined using experiments of DPPH radical scavenging activity (EC50 value 1.07 mg/ml) and total antioxidant capacity (19 μg AAE/mg of extract). Phytochemical screening of the methanolic extract revealed high contents of phenolics which was confirmed by HPLC and HPTLC studies. Rf values and their corresponding peaks serve as a signature marker for identification of this mushroom. On the other hand, molecular studies including DNA extraction and sequencing of the Internal Transcribed Spacer region of the genomic DNA serve as a molecular standard. The above distinctive parameters would significantly serve towards establishing the pharmacognostic as well as molecular standards for identification, authentication and quality control of the genuine mushroom. © 2016, Institute of Korean Medicine, Kyung Hee University and Springer Science+Business Media Dordrecht.