Abstract: Objective: To choose appropriate extraction method of total DNA of yellow rice wine and analyze its fugal diversity.Methods: Because of its character,different methods detection were compared and analyzed in this study,including total DNA purity,yield and gel electrophoresis combining with previous DNA extraction method.Objective bands were purified and quantified after PCR amplification of fungi primer,and conducted biological information analysis after Miseq high throughput sequencing.Results: Experimental result showed that kit + Physical+ enzyme method could get better quality and concentration fungal DNA,A_(260)/ A_(280) ratio was close to the ideal level,and could get obvious target band figure after PCR amplification gel electrophoresis. OTU classification,Shannon diversity curve and phylogenetic tree graph showed fungal diversity.Conclusion: Through the comparison and analysis of data,established method in this paper was an ideal method to extract total DNA in the rice wine wheat starter,determination of the fungal community also provided a powerful tool for later developing rice wine microbial resources.