Most strains harboring the feathered (fe) mutation in the Japanese morning glory (Ipomoea nil or Pharbitis nil) show deformed phenotypes such as upcurled leaves and separated or tubular petals. These phenotypes seem to be caused by loss of abaxial identity in lateral organs. The FE gene was isolated using the inserted transposon as a tag. An En/Spm-related transposable element, Tpn102, inserted in the fourth intron of the FE gene, was responsible for the fe mutation. FE encodes a GARP transcription factor closely related to Arabidopsis KANADI1 (KAN1), which promotes an abaxial cell fate. Genetic analyses and molecular studies, which showed that all fe mutant strains have the same fe allele despite their phenotypic differences, revealed that fe strains with strong phenotypes have additional mutations enhancing the fe phenotype. These findings and historical records of fe phenotypes suggest that these enhancer mutations were accumulated in the fe background during selection for strong phenotypes. The mutant phenotypes and molecular analysis of fe strains suggest that FE regulates the abaxial identity of lateral organs redundantly with modifier genes, as KAN1 does in Arabidopsis. FE, however, affects flower phenotype even in the single mutant unlike KAN1, moreover, modifier mutations affect flower phenotype only in the fe mutant background, suggesting that FE may play a more crucial role in promotion of abaxial cell fate in flowers of the Japanese morning glory.