Flowering at the right time requires the perception and processing of a diverse range of environmental and internal signals. Ninety-five soybean cultivars were used for this study. Eight ESTs relating flowering genes were selected from the soybean cDNA library in NCBI and TIGR. Primer 3 was used to design EST fragments of 500-800bp. Seven ESTs detected 39 different SNP positions. All genes contained exon region except gene Cry 02. Besides, Cop 01 ESTs contained both exon and intron regions. The same ESTs gave different LD among cultivar groups. The LD decay showed that it varied from one cultivar group to another, and from one EST to another. The flowering time of soybean varies a lot from one place to another. Therefore, gene variation at the nucleotide level will be useful for breeders to make a strategy for soybean improvement in the future.