A survey of petal-specific proteomes of soybean (Glycine max (L.) Merr[Non-italic].) was conducted comparing protein expression profiles in different petals. Two-dimensional polyacrylamide gel electrophoresis reference maps of protein extracts from standard petals (SP), lateral wings (LW), keel petals (KP), and reproductive organs (RO) (a mixture of stamen and carpel) were obtained. Protein expression in the three petal types was compared using Image Master TM 2D platinum 6.0 software. This indicated that the proportion of homologous proteins between SP and LW was 59.27％, between SP and KP was 61.48％, and between LW and KP was 60.05％. Within a mass range of 6.5-200.0 ku and pH 4.0-7.0, approximately 590, 646, 544, and 700 protein spots were detected in SP, LW, KP, and RO, respectively. A total of 82 differentially expressed proteins were detected. Sixty-four of these detected spots were differentially expressed and showed more than 2-fold changes in abundance; of these 64 proteins, 26 showed increased expression and 38 showed decreased expression. Among these spots, single organ-specific proteins were also identified. They were ID 49 (60.9 ku), ID 45 (50.0 ku), and ID 46 (40.5 ku) in RO, ID 98 (42.0 ku) in SP, and ID 05 (29.0 ku) in KP. A total of 14 protein spots from 82 differentially expressed proteins were identified with LC-MS/MS. Further protein identification was conducted using the SwissProt and NCBInr databases. The identified proteins and their putative functions were discussed further. This was the first study reporting the comparison of petal protein profiles of soybean florets using proteomics tools.