The hormonal action of jasmonate in plants is controlled by the precise balance between its biosynthesis and catabolism. It has been shown that jasmonyl-L-isoleucine (JA-Ile, 6) is the bioactive form involved in the jasmonate-mediated signaling pathway. However, the catabolism of JA-Ile (6) is poorly understood. Although a metabolite, TA-Ile (7), has been characterized, detailed functional studies of the compound and the enzyme that produces it have not been conducted. In our results, the kinetics of wound-induced accumulation of TA-Ile (7) in plants was examined, and its involvement in plant wound response is described. Candidate genes for the catabolic enzyme were narrowed down from 272 Arabidopsis cytochrome P450 genes using Arabidopsis mutants. The candidate gene was functionally expressed in Pichia pastoris to reveal that CYP94B3 encodes JA-Ile (6) 12-hydroxylase. Expression analyses demonstrate that expression of CYP94B3 is induced by wounding and shows the activity toward JA-Ile (6). Plants grown in medium containing JA-Ile (6) show higher sensitivity to JA-Ile (6) in cyp94b3 mutants than in wild-type plants. These results demonstrate that CYP94B3 plays a major regulatory role in controlling the level of JA-Ile (6) in plants. CYP94B3 can use other JA-amino acid conjugates as substrates. Our other results uncovered that JA amino acid conjugates induced by wounding, JA-Phe and JA-Val, possessed biological activities same as JA-Ile (6).