A proteomics approach was applied to analyze differential expression of proteins in wild (Glycine soja) and cultivated (Glycine max) soybean seeds. Two-dimensional gel electrophoresis (2-DE) with immobilized pH gradient (IPG, ranges 4～7) strips was used to separate proteins. On the 2-DE gels stained by Coomassie brilliant blue, PDQuest image software detected about 550 protein spots, of which 10 spots show more than 2.5-fold changes in abundance between wild and cultivated soybeans. These 10 proteins treated by tryptic in-gel digestion were characterized by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and peptide mass finger printings of all were obtained. Soybean UniGene database and NCBI were used to identify proteins, of which 5 proteins were identified. They were soybean agglutinin, seed maturation protein PM24, maturation polypeptide, sucrose-binding protein precursor and trypsin inhibitor p20. The potential functions of these identified proteins were discussed.