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Wasabi (Japanese horseradish) is used extensively in Japanese cuisine because of its characteristic flavour. The plant is grown as a perennial crop in New Zealand. The rhizomes are the most sought after part of wasabi although other parts of the plants are pungent. In this study the yields of individual and total isothiocyanates (ITCs) were measured in the four main parts of the plant: root, rhizome, petiole and leaves in mature, flowering and non-flowering, 18-month-old plants. The plants were grown without fertilizer in beds flooded with river water. The total ITC and individual contents of allyl, 3-butenyl, 4-pentenyl and 5-hexenyl ITC in the roots and rhizomes of the flowering plants were all significantly higher (P<0.001) than in the comparable non-flowering plant parts. The level of total ITC in the epidermis and cortex of rhizomes of the flowering plants was 3144 mg/kg fresh weight basis compared to 1773 mg/kg in the non-flowering tissue. The total ITC contained in the vascular and pith tissue was 2234 mg/kg fresh weight for the flowering plants compared to 1388 mg/kg fresh weight for the non-flowering plants. Such differences between the ITC profiles in the flowering and non-flowering tissue of wasabi plants suggest there will be differences in the overall aroma profiles when the material is made into a processed product. The magnitude of such differences suggest the flowering state of wasabi plants could be important in crop management for optimal processing quality. [Copyright &y& Elsevier]