The pungent flavor unique in wasabi is due to isothiocyanates including allyl isothiocyanate (AIT) which has outstanding antimicrobial activity. AIT is converted from sinigrin by enzymatic reaction in the presence of water. The optimum moisture content of wasabi root for supercritical $CO_2$ extraction (SCE) at 20 MPa and $35^{circ}C$ was found to be 125% dry basis. In the ranges of pressure (15-25 MPa) and temperature ($35-55^{circ}C$), yield of AIT by SCE increased as pressure increased and/or temperature decreased. The highest yield was 408 mg/100 g solid at 25 MPa and $35^{circ}C$. SCE of AIT from the freeze-dried wasabi root, stem, and leaf at 20 MPa and $35^{circ}C$resulted in the yields of 368, 39, and 11 mg/100 g solid, respectively. The moisture content of wasabi along with the pressure and temperature were the important parameters in SCE of AIT.