[Background] Shangri-La wine-producing region of Yunnan is located in the Three Parallel Rivers National Park, and its microbial resources are abundant. The variety of wild-yeasts associated with wine making is also very diverse. [Objective] To study the diversity of yeasts and the genetic diversity of Saccharomyces cerevisiae in Shangri-La wine-producing region. [Methods] Five vineyards from the Shangri-La Jinsha River and Lancang River were selected to collect ripe grape samples and separate the yeasts from the grape peel and fermentation process. The yeast species were identified by WL (Wallerstein laboratory nutrient agar) identification medium and 26S rDNA D1/D2 domain sequence analysis. The genetic diversity of S. cerevisiae was studied by SSR molecular markers. [Results] a total of 230 wild yeasts isolated from grape berries were identified as 13 genera and 18 species, of which 10 species were found for the first time in Shangri-La. Genetic diversity of 47 S. cerevisiae strains was analyzed by SSR molecular markers, and 47 strains of S. cerevisiae were divided into 24 genotypes. 70 alleles were observed by microsatellite markers among the 47 strains. The average polymorphism information content (PIC) was 0.640. The mean observed heterozygosity (Ho) was 0.166, and the mean expected heterozygosity (He) was 0.693. [Conclusion] There are abundant yeast resources in the Shangri-La Wine-producing region, which shows the high species diversity of yeast and moderate genetic diversity of S. cerevisiae. Study on the diversity of yeast in this area, it aims to lay a foundation for the conservation and utilization of the diversity of Shangri-La’s yeast resources.