Anthocyanins are important plant pigments that fulfil many physiological and ecological functions. Anthocyanin biosynthesis is controlled by numerous regulatory factors at the transcriptional level. Jasmonates (JAs) has been shown to induce anthocyanin accumulation in several plant species, however, the molecular mechanism for JA-regulated anthocyanin accumulation remains unknown. In this study, genetic, molecular, and physiological approaches were used to reveal the molecular basis of JA-regulated pigmentation in Arabidopsis. It was found that the F-box protein COI1 was required for JA-specific induced expression of the 'late' anthocyanin biosynthetic genes DFR, LDOX, and UF3GT. It is further demonstrated that COI1 was essential for JA-induction of transcription factors PAP1, PAP2, and GL3. It is speculated that COI1 regulates the expression of the transcription factors, including PAP1, PAP2, and GL3, which mediates the 'late' anthocyanin biosynthetic genes DFR, LDOX, and UF3GT, thereby modulating JA-induced anthocyanin biosynthesis in Arabidopsis.