Honey is widely produced in China as a natural health food with high nutritional value. In this study, high-throughput sequencing (HTS) and culture-dependent methods were used to assess the yeast diversity of wild honey from three different regions of Xinjiang. The analysis of HTS data of 26S rDNA NL1F and NL2R region genes revealed the highest number of operational taxonomic units (OTUs) of the yeast genus Zygosaccharomyces in honey, followed by the genera Aureobasidium and Clavispora. Multifloral honey is not only different in yeast structure and composition from monofloral honey, but also more diverse than monofloral honey. Thirty-five yeast strains were obtained by traditional isolation and culture methods, and morphological, physiological and biochemical, and 26S rDNA D1/D2 domain genes were sequenced to identify 11 yeast species, including Zygosaccharomyces siamensis, Aureobasidium pullulans, Naganishia albida, Saccharomyces cerevisiae, Wickerhamomyces anomalus, Rhodotorula glutinis, Pichia kluyveri, Barnettozyma californica, Rhodotorula kratochvilovae, Candia tropicalis, Pichia terricola, and these results are not entirely consistent with those obtained using high-throughput sequencing methods. Different species of honey may have contributed to the diversity of yeast. The results of this study provide basic information on the yeast diversity of native honey in Xinjiang, which will help to develop germ plasm resources of yeast in honey.