Mutations in a floral homeotic gene DUPLICATED (DP) in the Japanese morning glory (Ipomoea nil) cause a substitution of reproductive organs to perianth organs (petals and sepals). This phenotype is similar to loss-of-function phenotypes of the C-function MCM1, AGAMOUS, DEFICIENS and SRF (MADS)-box gene family of transcription factors. DP was isolated using the consensus sequence of C-function MADS-box genes. Its intron-exon structure was well conserved beyond species, and it belongs to the FARINELLI (FAR)-pMADS3 subclass of C-function MADS-box genes. In a dp mutant, an Enhancer/Suppressor-mutator (En/Spm)-related transposable element, transposable element of Pharbitis nil (Tpn)-botan, was inserted in the second intron of DP gene, and the subsequent excision event led to a deletion of a substantial part of the original Tpn element and DP genome. A segment of Tpn1-related transposable element was identified at the recent insertion site of the wild-type DP genome. This transposable element sequence was present in all Ipomoea species tested. This finding suggests that the insertion event originated in an ancestral species of genus Ipomoea.