In order to accurately identify Enterococcus faecalis and Enterococcus faecium isolated from natural fermented dairy products,in this study,four identification methods,namely traditional physiological and biochemical identification methods,16S rRNA gene analysis,16S-23S rRNA Intergenic spacer region polymorphism and Denaturing Gradient Gel Electrophoresis were carried out to differentiate the tested strains.Meanwhile,the identification of these four methods was compared with evaluated ability.The results showed that except for the methods of the traditional physiological and biochemical identification methods and 16S rRNA gene analysis,16S-23S rRNA Intergenic spacer region polymorphism and Denaturing Gradient Gel Electrophoresis not only were competent,but also could divide Enterococcus faecalis and Enterococcus faecium into different kinds of gene isoforms.