Abstract: Bacillus subtilis subsp. natto BEST195 is one of the important strains produced natto. To identify the secreted protein from Bsubtilis and clearly it′s characteristic. 4456 protein sequences in Bsubtilis was analyzed to find the secreted protein using the program including SignalP, ProtComp, TMHMM, Phobius, LipoP and TatP. Meanwhile, the distribution of amino acids, the length of signal peptide as well as the signal peptide cleavage site of secreted protein was analyzed. 102 secrete proteins were found in Bsubtilis. And the length of amino acids and the signal peptide were different the plant pathogens. The signal peptide cleavage site belongs to AXA type, which was same as other plant pathogenic fungi, bacteria and oomycete. Through the above bioinformatics analysis, the predicted secreted proteins can effectively achieve in Bsubtilis, and the type of signal peptide cleavage site have consistent with other secreted proteins from different species.