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Wasabi japonica plantlets were acclimatized in a hydroponic system to determine effective procedures. The plantlets were cultured on solid Murashige-Skoog medium with 3% sucrose. Shoots that formed roots were transplanted into hydroponic systems: 1) acclimatization in ebb-and-flow (EBB) for subirrigation (medium: granulated rockwool and coir); and 2) acclimatization in deep flow technique (DFT). The plantlets were acclimatized for 5 weeks under two irradiance treatments, 50 and 300 mmol·m-2·s-1. Photosynthetic capacity in high PPF was higher than that in low PPF during acclimatization. Electron transport rate from PS II (ETR) and biomass production increased significantly with increased light availability. The fresh weight, dry weight, and leaf area of plantlets in high PPF were higher than those in low PPF. In particular, the dry weight and ETR of the plantlets grown in high PPF increased more than twice as much as those in low PPF. At 50 mmol·m-2·s-1 PPF, growth indexes, such as number of leaves, leaf length, leaf width, leaf area, fresh weight, and dry weight, were higher in EBB (granulated rockwool) > EBB (coir culture) > DFT. At 300 mmol·m-2·s-1 PPF, those indexes were higher in DFT > EBB (granulated rockwool) > EBB (coir). The Wasabi japonica plantlets acclimatized in a hydroponic system also had a superior performance when they were transferred to the field.