Abstract: Objective: Establishing a method based on Illumina Miseq deep sequencing to analyze the microbial diversity of yogurt. Methods: Took 9 kinds of yogurt samples as the research objects and extracted the whole genome of bacteria of yogurt. The v1- v3 variation region of 16 S r DNA were detected by high throughput sequencing technology to obtain the distribution and abundance of microbial community in 9 samples as well as the species difference and evolution relationship of bacteria among these samples.Results: The results showed that the main microbes of the yogurt were Firmicutes( 99.6%) which mainly composed by Streptococcus( 87.1%),Lactobacillus( 10.3%),and Lactococcus( 0.3%).There were 3 kinds of yogurt containing Streptococcus and Lactobacillus with a high number,Streptococcus( 97%) accounted for almost all in the other six samples.Conclusion: Using Illumina Miseq deep sequencing technology can master the microbial diversity of yogurt quickly and accurately. The results showed that the bacteria of yogurt were highly similar and streptococcus took a dominant position.At the same time,it was found that some yogurt labels didn't match the analysis results well.