[Objective] To explore the effects of spontaneous and inoculated wine fermentations on the yeast diversity and genetic diversity of Saccharomyces cerevisiae. [Methods] Spontaneous and inoculated fermentations were conducted with Chardonnay using different S. cerevisiae strains of NXU17-26, UCD522 and UCD2610. We used 26S rDNA D1/D2 sequence analysis and Interdelta fingerprint to distinguish the yeasts at interspecific and intraspecific levels, respectively. The diversity of S. cerevisiae strains was analysed by cluster analysis and diversity index. [Results] The fermentation curve of spontaneous fermentation was relatively smooth, and the fermentation speed of inoculated fermentations was significantly faster than spontaneous fermentation. The isolated yeasts were identified as 6 genera and 11 species with 6 species of 5 genera of non-Saccharomyces in spontaneous fermentation. The yeast diversity in inoculated fermentation was far lower than that in spontaneous fermentation, which was composed of Saccharomyces cerevisiae and two non-Saccharomyces. UCD2610 dominated the corresponding fermentation and its genotype accounted for 48.78%; while in the fermentation inoculated with NXU17-26 and UCD522, we didn't find the same genotype as them. Genetic differences between Saccharomyces cerevisiae strains isolated from UCD522 fermentation were small, while obvious in NXU17-26 and UCD2610 fermentations. Diversity index results showed that UCD2610 showed a more prominent position in the fermentation; Saccharomyces cerevisiae strains isolated in UCD522 fermentation showed a higher diversity, and there were more unknown factors affecting the population diversity and the concentration of different genotypes of Saccharomyces cerevisiae. [Conclusion] Fermentation methods have a significant effect on the yeast diversity and the genetic diversity of Saccharomyces cerevisiae strains. This study provides reference for the control of microorganisms during wine fermentation.