Shalgam is a fermented beverage obtained by lactic acid fermentation and its quality depends on flora. Therefore, it is essential to be able to characterize yeasts, in order to improve the quality and safety controls of final products. This study aimed to identify endogenous yeasts found during the fermentation of shalgam and to determine their technological properties. 172 yeast isolates were obtained and the DNA fingerprints were constituted by iPBS-PCR method. Sequencing of ITS regions of different groups revealed the species of Pichia kudriavzevii, P. fermentans, Saccharomyces cerevisiae, Candida oleophila, Kazachstania bulderi, and Geotrichum candidum. Interestingly, the prevalence of P. kudriavzevii in the flora increased during the fermentation, while the other species decreased. To determine the preliminary technological properties of yeasts, their development at different conditions was examined and 31 technologically superior strains were determined by Principal Component Analysis (PCA). Among these, 17 P. kudriavzevii strains had a vigorous fermentation rate and selected to assess their enzymatic activity. The isolates had diverse enzyme activities, including esterase, esterase lipase, and leucine arylamidase, which may have crucial roles for aroma formation. According to the results, P. kudriavzevii 3-3S9, 3-3S2, and 3-3Y1 strains were selected to be candidate starters for shalgam production.