Abstract: PCA is a normal method used for Biolog ECO and DGGE data analysis.However,this method hardly distinguishes soil microbial diversity structure and microbial markers in different environments.In this study,PCA,PLS-DA,PLS-EDA methods were used to study microbial diversity structure in different environments.PLS,OPLS methods were used to discover microbial makers.The results showed that:PLS-EDA method completely separated microbial diversity structure in different environments(PC1=16.8%),one sample could not be completely separated by PLS-DA(PC1=33%),but PCA was not good method to microbial diversity structure for DGGE data analysis.PLS-EDA completely separated microbial diversity structure different environments(PC1=25.5%),one sample could not be completely separated by PLS-DA(PC1=36.3%),also,PCA was not good method to microbial diversity structure for Biolog ECO data analysis.PLS and OPLS were selected for microbial makers,both methods were suited for underlying microbial makers.In conclusion:PLS-EDA was an optimum method to distinguish different environments soil samples.PLS and OPLS may develop as methods to select underlying microbial makers.