Plants exhibit different flowering behaviors in response to variable photoperiods across a wide geographical range. Here， we identify MYC3， a bHLH transcription factor， and its cis-element form the long-sought regulatory module responsible for?cis-regulatory changes at the florigen gene FLOWERING LOCUS T (FT) that mediate natural variation in photoperiodic flowering responses in Arabidopsis. MYC3 is stabilized by DELLAs in the gibberellin pathway to suppress FT through binding the ACGGAT motif and antagonizing CONSTANS (CO) activation. Changing photoperiods modulate the relative abundance of MYC3 and CO， thus determining either of them as the predominant regulator for FT expression under different day lengths. Cis-regulatory changes in the MYC3 binding site at FT are associated with natural variation in day-length requirement for flowering in Arabidopsis accessions. Our findings reveal that environmental and developmental signals converge at MYC3 suppression of FT， an elementary event underlying natural variation in photoperiodic flowering responses.