Abstract: Denaturing gradient gel electrophoresis ( DGGE) technique were applied to analyze the interaction between Kluyveromyces marxianus and the lactic acid bacteria during fermentation and storage process for tracking and monitoring advantages microbial flora and microbial stability. The results showed that during mixed fermentation and storage process, microbial composition was relatively stable, Streptococcus thermophilus was regarded as dominant flora. Mixed fermentation process, the growth of lactic acid bacteria were promoted by adding Kluyveromyces marxianus, especially Lactobacillus bulgaricus, while the growth of lactic acid bacteria was inhibited in storage.The whole process, yeast growth was inhibited by lactic acid bacteria. This study provided a theoretical basis for further research on the mechanism of lactic acid bacteria and yeast fermentation and development of new fermented dairy products.