The speckled mutant of the Japanese morning glory blooms pale yellow flowers with fine and round colored spots, or speckles, distributed over the corolla. Since it also occasionally produces flowers with colored sectors apparently due to somatic mutations, the mutable speckled allele is thought to carry a transposable element. In this paper, we show that the appearance of the variegation phenotypes in the speckled mutant was controlled not only by the recessive speckled allele but also by a dominant genetic element, termed speckled-activator. Our results also indicated that the recessive c-1 mutation affecting pigmentation of flowers and mapped near the speckled locus causes a defect in a regulatory gene controlling the expression of structural genes for anthocyanin biosynthesis.