In our study, spontaneous alcoholic fermentations were carried out to isolate non- and yeasts from grape must from different vine-growing regions in Slovenia. Additionally, the diversity of native strains was evaluated during the process. During spontaneous alcoholic fermentations the yeast population of non- and yeasts was sampled. We used eleven microsatellite markers to determine the genetic diversity of strains. In addition, different ratios of the indigenous strains of , and were tested for their possible use in alcoholic fermentation with inoculated yeasts by monitoring its course and measuring the concentration of aroma compounds in wine. Sequencing of the internal transcribed spacer (ITS) regions of ribosomal DNA showed that of 64 isolates, 46 strains represent and 18 strains belong to non- yeasts. The identified non- yeast species were , , and . The dendrogram grouped strains into 14 groups. The number of strains isolated from the musts was 10 (Posavje), 11 (Podravje) and 25 (Primorska vine-growing region). On the other hand, the alcoholic fermentation with inoculated yeasts, in which the native strain predominated over and , gave the most promising result due to the highest alcoholvolume fraction, the lowest acetic acid concentration and significantly higher concentrations of volatile thiols 3-mercaptohexyl acetate (3MHA) and 3-mercaptohexan-1-ol (3MH), 2-methylpropanol, 2-methylbutanol, 3-methylbutanol and 2-phenylethanol) in the produced wine. We confirmed the potential use of indigenous and non- yeasts in alcoholic fermentation with inoculated yeasts, which allows the positive properties of the yeast strains to be expressed and good quality wines to be produced. Thus, the results are encouraging for winemakers to create different wine styles associated with a particular terroir using indigenous yeasts.