To clarify the genetic factor underlying the early flowering in soybean (Glycine max L.) cultivar BeiNong103, F2 segregating population from a cross of cv. BeiNong103 (male) and cv. Haixi13 (female, late-flowering) as well as its derived F2: 5 recombine inbred line population were subjected for analyzing the segregation ratio and the preliminary mapping following the bulked-segregant analysis pipeline. The genetic analysis suggested a single recessively-inherited locus on chromosome 6, which is associated to the early-flowering phenotype in cv. BeiNong 103. The genetic interval, franked by two markers Satt557 and XH2_11, expanded 2 cM which harbors a formerly-identified recessive gene el of E1. The sequence analysis showed a G to C mutation at the 218bp of E1 coding sequence, thus resulting in an amino acid substitution of arginine (AGG) to threonine (ACG) in BeiNong103. Taken together, the single-base mutation of e1 might be the causal agent that underlies the sensitivity of the photoperiod and the early flowering. The elite allele, suggested by the pedigree analysis, is derived from the American variety Century, and might play a role in future improvement of the maturity and plant height characteristics of cultivar in soybean breeding.