This article presents the first report on systematic synthesis and evaluation of activated carbons from the cap and stalk of two diverse mushroom species namely, Ganoderma lucidum (GL) and Calocybe indica (CI) belonging to different classes white rot and brown rot respectively. A novel microwave induced H3PO4 activation followed by carbonization and KOH activation enabled the formation of activated carbon with hierarchical structures. The activated carbons from cap and the stalk of the mushrooms are different in terms of specific surface area, pore volume, and their electrochemical behavior. Specific surface area and pore volume from GL‐cap is as high as 2432.4 m2/g and 0.54 CC/g, respectively. After optimization, the activated carbons have high graphitic content, good thermal stability and show specific capacitance as high as 271.94 F/g, energy and power densities of 13.59 Wh/kg and 127.31 W/kg, respectively. All the carbons show good capacitance retention up to 10 000 cycles. The surface area and specific capacitance in the mushroom stalks are lower than the ones made from the caps and the highest surface area and specific capacitance are 1576.2 m2/g and 137.2 F/g respectively for GL‐stalk.