Abstract: LC/Q-TOF MS has been applied to the metabonomics analysis of Bacillus.Significant potential metabolic markers were developed by analyzing different species of Bacillus,hierarchical clustering and PCA analysis were used for classification of various Bacillus and PLS-DA prediction model was established.The results showed that there were statistical difference between Bacillus mycoides and Bacillus subtilis.Resultssuggested that metabonomics was a potential classable method to the identification of bacillus.