Plants belong to the section Mina showed characteristic petal pigmentation among Ipomoea plants. For example, petals of Ipomoea hederifolia var. lutea display yellow color derived from carotenoids and those of Ipomoea quamoclit display red color derived from pelargonidin-based anthocyanins. In this study, the pigment composition and the expression patterns of genes for pigment biosynthesis in the petals of I. quamoclit and I. hederifolia var. lutea were analyzed to elucidate the crucial factors that determine petal color in section Mina. The petals of white-flowered I. quamoclit lack the ability to synthesize anthocyanins and carotenoids because of the suppression of anthocyanidin synthase (ANS) gene expression and transcriptional down-regulation of multiple carotenogenic genes, respectively. In petals of I. hederifolia var. lutea, the absence of dihydroflavonol 4-reductase (DFR) gene expression is responsible for the lack of anthocyanins. All F1 progeny obtained by interspecies crossing between I. quamoclit and I. hederifolia var. lutea had scarlet petal color produced by a combination of pelargonidin-based anthocyanins and carotenoids. The flavanone 3-hydroxylase gene, DFR, and ANS were expressed in the petals of the F1 progeny. The results suggest that in these section Mina species, the carotenoid-accumulating phenotype in petals is dominant, and that pelargonidin was produced in the F1 progeny by complementary expression of DFR from white-flowered I. quamoclit and ANS from I. hederifolia var. lutea.