Abstract:S. roseoflavus Men-myco-93-63 isolated from potato scab decline soil is an antagonistic strain. The strain and it’s fermentation can inhibit many phytopathogenic fungi and control the related important plant disease such as cotton verticillium wilt, cumber powdery mildew, and so on. The total protein of S. roseoflavus Men-myco-93-63 and its high-yield antibiotic strain D12-3 were analyzed by two-dimensional gel electrophoresis. As the results, a modified 2-DE protocol and modified electrophoresis program suitable for Men-myco-93-63 were developed in the study. Four different expression protein spots were isolated and identified by Matrix-Assisted Laser Desorption Ionization (MALDI) Time-of-Flight (TOF) mass spectrum. The results show the proteins are PhaP, Beta-lactamase, methyl-accepting chemotaxis protein, and ABC transporter, respectively, which perhaps are related with the biosynthesis of antibiotic of S. roseoflavus Men-myco-93-63.