Since the genome sequences of wild species may provide key information about the genetic elements involved in speciation and domestication, the undomesticated soybean (Glycine soja Sieb. and Zucc.), a wild relative of the current cultivated soybean (G. max), was sequenced. In contrast to the current hypothesis of soybean domestication, which holds that the current cultivated soybean was domesticated from G. soja, our previous work has suggested that soybean was domesticated from the G. soja/G. max complex that diverged from a common ancestor of these two species of Glycine. In this review, many structural genomic differences between the two genomes are described and a total of 705 genes are identified as structural variations (SVs) between G. max and G. soja. After protein families database of alignments and hidden Markov models IDs and gene ontology terms were assigned, many interesting genes are discussed in detail using four domestication related traits, such as flowering time, transcriptional factors, carbon metabolism and disease resistance. Soybean domestication history is explored by studying these SVs in genes. Analysis of SVs in genes at the population-level may clarify the domestication history of soybean.