Japanese morning glory,Ipomoea nil, exhibits a variety of flower colours, except yellow, reflecting the accumulation of only trace amounts of carotenoids in the petals. In a previous study, we attributed this effect to the low expression levels of carotenogenic genes in the petals, but there may be other contributing factors. In the present study, we investigated the possible involvement of carotenoid cleavage dioxygenase (CCD), which cleaves specific double bonds of the polyene chains of carotenoids, in the regulation of carotenoid accumulation in the petals ofI. nil. Using bioinformatics analysis, sevenInCCDgenes were identified in theI. nilgenome. Sequencing and expression analyses indicated potential involvement ofInCCD4in carotenoid degradation in the petals. Successful knockout ofInCCD4using the CRISPR/Cas9 system in the white-flowered cultivar I. nil cv. AK77 caused the white petals to turn pale yellow. The total amount of carotenoids in the petals ofccd4plants was increased 20-fold relative to non-transgenic plants. This result indicates that in the petals ofI. nil, not only low carotenogenic gene expression but also carotenoid degradation leads to extremely low levels of carotenoids.