Abstract:[Background] Ganzi, an alpine wine region in southwestern China, enjoys favorable natural conditions for making wine. [Objective] To study the diversity of eukaryotic microorganisms, the genetic diversity of native Saccharomyces cerevisiae, and the diversity of native yeasts under the influence of commercial yeasts in the Ganzi wine region. [Methods] Cabernet Sauvignon grapes were grouped for Inoculated fermentation and natural fermentation. Then, Internal Transcribed Spacer (ITS) high-throughput sequencing was used to analyze the diversity of microorganisms during fermentation, and Interdelta fingerprinting was employed for classifying the genotypes of wild S. cerevisiae identified by 26S rRNA gene. [Results] Yeasts in 7 genera of 7 families in the natural fermentation and Inoculated fermentation were respectively identified, and Interdelta fingerprinting showed 5 genotypes of S. cerevisiae in Ganzi wine region. According to the phylogenetic tree of 6 representative S. cerevisiae strains in the Ganzi wine region and 109 S. cerevisiae strains from other producing areas in China, the 6 strains were in close genetic relationship with those from Beijing. [Conclusion] Ganzi wine region is rich in yeast resources, showing high microbial diversity and moderate genotypic diversity of native S. cerevisiae, which presents a potential for searching excellent native strains.