[Objective] The aim is to study the genotype diversity of indigenous Saccharomyces cerevisiae isolated from spontaneous fermentations of Vitis davidii Föex in Ziyun County of Guizhou Province, to analyze the dynamic changes of different S. cerevisiae genotypes at different fermentation periods, and to provide theoretical references for the industrial application of excellent S. cerevisiae resources. [Methods] We applied interdelta fingerprinting analysis and microsatellite marker analysis to study the genotype diversity of indigenous S. cerevisiae during spontaneous fermentations of Vitis davidii Föex in Ziyun County of Guizhou Province. DPS software was used to analyze the genetic relationship among different genotypes. [Results] We totally isolated 75 indigenous S. cerevisiae strains, and identified them into 10 genotypes by interdelta fingerprinting analysis and microsatellite marker analysis. Genotypes 6, 9, 10, 11, 14, 15 and 16 are the peculiar seven genotypes owned by indigenous S. cerevisiae strains. Genotypes 7, 17 and 18 are the mutual three genotypes owned by both indigenous and commercial S. cerevisiae strains. Furthermore, other commercial S. cerevisiae strains in the study showed nine other specific genotypes including genotypes 1, 2, 3, 4, 5, 8, 12, 13 and 19. The genotype 17 took the highest proportion in the 75 isolates (36%) followed by the genotype 10 (13.3%). Different genotypes showed waxing and waning ratio changes during fermentations, and the cell density of each genotype varied among 10⁴-10⁷CFU/mL. [Conclusion] Spontaneous fermentation samples of Vitis davidii Föex in Ziyun County of Guizhou Province showed rich genotype diversity of S. cerevisiae strains. Genotypes 10 and 17 were the predominant S. cerevisiae genotypes. This study laid a basis for the development of excellent indigenous S. cerevisiae resources of Vitis davidii Föexin Guizhou Province.