To increase the safety and quality of baijiu and rice wine in China, controlling the use of traditional
Xiaoqu
by studying the beneficial yeasts present has recently been considered. The fungal diversity of six Chinese
Xiaoqu
including five traditional and one commercial samples was investigated to screen fermentative yeasts with low yields of higher alcohols. A high throughput sequencing approach detected fifteen fungal species with relative abundance higher than 1%, and displayed dissimilarities of fungal diversity among
Xiaoqu
samples. The 15 fungal species were composed of 11 filamentous fungi with
Rhizopus arrhizus
as the most common specie and four yeast species, containing
Hyphopichia burtonii
,
Saccharomyces cerevisiae
,
Saccharomycopsis fibuligera
, and
Saccharomycopsis malanga
. Classic culture-dependent approaches, including 5.8S-ITS-RFLP analysis and D1/D2 sequencing of the 26S rRNA gene, identified nine yeast species in the five traditional Chinese
Xiaoqu
. In addition to the four yeast species also detected by high throughput sequencing approach, the other five yeast species isolated were
Clavispora lusitaniae
,
Cryptococcus neoformans
,
Komagataella pastoris
,
Trichosporon asahii
, and
Wickerhamomyces anomalus
. Further micro-fermentations of rice wine were performed using 19 single yeast isolates, and after the fermentation of rice wine, higher alcohols and ethanol were analyzed by gas chromatography. Two yeast strains,
Saccharomyces cerevisiae
FBKL2.8022 and
Wickerhamomyces anomalus
FBKL2.8023, were found to have low yields of higher alcohols and could produce 11.70%vol and 7.10%vol ethanol separately. This study for the first time, to the best of our knowledge, explored the fungal resources in traditional
Xiaoqu
from different regions of Guizhou, China. The screened
S. cerevisiae
and
W. anomalus
strains could be used to establish specific starters to promote the standardization of the production of baijiu and rice wine.