Flowering and dwarfism induced by 5-azacytidine and zebularine, which both cause DNA demethylation, were studied in a short-day (SD) plant Pharbitis nil (synonym Ipomoea nil), var. Violet whose photoinduced flowering state does not last for a long period of time. The DNA demethylating reagents induced flowering under non-inductive long-day (LD) conditions. The flower-inducing effect of 5-azacytidine did not last for a long period of time, and the plants reverted to vegetative growth. The progeny of the plants that were induced to flower by DNA demethylation did not flower under the non-inductive photoperiodic conditions. These results suggest that the flowering-related genes were activated by DNA demethylation and then remethylated again in the progeny. The DNA demethylation also induced dwarfism. The dwarfism did not last for a long period of time, was not heritable and was overcome by gibberellin A3 but not by t-zeatin or kinetin. The change in the genome-wide methylation state was examined by methylation-sensitive amplified fragment length polymorphism (MS-AFLP) analysis. The analysis detected many more polymorphic fragments between the DNA samples isolated from the cotyledons treated with SD than from the cotyledons under LD conditions, indicating that the DNA methylation state was altered by photoperiodic conditions. Seven LD-specific fragments were extracted from the gel of the MS-AFLP and were sequenced. One of these fragments was highly homologous with the genes encoding ribosomal proteins.