This review summarizes the current status of application of functional and structural proteomic strategies for bacteria belonging to the species Bacillus and their applications in life science research. Structural proteomics plays a crucial role for studying the relationship between structures and functions of proteins. In addition, bioinformatics is very useful for rapid search of unknown proteins including their functions, and interpretation of data in both genomics and proteomics. Expression proteome analysis based on advanced and high throughput technologyis available now is important for quantifying and analyzing protein or gene expression and understanding their biological functions. Such analysis is currently possible by the application of various multidimensional techniques, such as two-dimensional (2-D) gel electrophoresis, mass spectrometry (MS), capillary electrophoresis (CE) and other related techniques. Proteome analysis has been extensively used to study the physiology as well as molecular mechanisms of responses of Bacillus under various stress condition such as heat, cold, acid, alkali, osmotic pressure and starvation to obtain important information for comprehensive study of protein and gene functions. The applications of proteomic analysis for biomarkers and drug discovery for Bacillus sp. and the future applications of proteomics for Bacillus have been discussed.