Soybean is a short-day plant, which means short day length promotes flowering. So far nine major loci, E1 to E8 and J, affecting the timing of flowering and maturity have been genetically identified in soybean. To understand the roles of soybean flowering genes in photoperiod-dependent flowering time control in soybean, we analyzed not only expression patterns of E1, E2, E3 and E4 genes as well as soybean FT homologs, including GmFT2a, GmFT5a and GmFT4, but also structural variation of E1, E2, E3, and E4 genes in various soybean accessions exhibiting a broad range of flowering time. The mRNA level of GmFT2a and GmFT5a was low in late flowering accessions, but high in late flowering accessions. In contrast, GmFT4 exhibited opposite expression pattern to those of GmFT2a and GmFT5a. Structural variation of E1, E2, E3 and E4 gene in these accessions revealed that early and moderate flowering accessions contained non-functional alleles of E1, E2, E3 and E4 genes in their genome. These results suggested that expression patterns of GmFT2a GmFT5a and GmFT4 would be important factor determining flowering time in soybean and allelic variation and genetic combination of upstream E1, E2, E3, and E4 genes would be more important in soybean flowering time control than their gene expression patterns.