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 soybean cDNA library in NCBI and TIGR. These ESTs were designed using Primer 3 to amplify 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. 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. There was wide variation in flowering time of soybean. Therefore, gene variation at nucleotide level will be useful for breeders to make strategy for soybean improvement in future.