Flowering time is a critical trait in common bean (Phaseolus vulgaris), influencing yield stability and geographical adaptation. While PvCOL2 and PvPHYA3 are known regulators under long-day (LD) conditions, we identified a third major locus through fine-mapping of the QTL DTF9.4/DTF9.5. Within this region, PvE1 (Phvul.009G204600) emerged as a strong candidate, sharing sequence homology with the soybean E1 gene and acting as a transcriptional repressor of flowering. A naturally occurring 34-bp deletion in its 3′ UTR (e1-del) was associated with early flowering and reduced photoperiod sensitivity. Expression analysis revealed that PvE1 displays a circadian rhythm under LD conditions, with a bimodal pattern peaking in the morning and early evening, resembling that reported for soybean E1. Phenotypic analyses of near-isogenic lines (NILs) confirmed that PvE1 delays flowering specifically under LD and also influences plant architecture, as e1 genotypes exhibited reduced plant height and node number. Functional dissection revealed that PvE1 and PvCOL2 act in partially redundant pathways to repress PvFT gene expression, with evidence of functional interaction. This regulatory module resembles that in soybean but shows species-specific divergence likely shaped by separate evolutionary paths. Genetic diversity analysis identified two rare PvE1 alleles, e1-del and e1-fs, both associated with earlier flowering when combined with col2 mutations, indicating additive effects and reduced photoperiod sensitivity. Although functional validation by transformation was not performed, the use of NILs provides robust genetic evidence of PvE1 activity. Together, these findings establish PvE1 as a conserved legume-specific floral repressor in common bean, with novel allelic variants that can be exploited to develop early-flowering, photoperiod-insensitive cultivars adapted to temperate and high-latitude regions.

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