Yakju, a traditional fermented beverage in Korea, is prepared using various raw materials and methods, and, hence, exhibits various characteristics. Low-temperature-fermented yakju can inhibit the growth of undesirable bacteria and is known for its unique flavor and refreshing taste. To increase the production of volatile aromatic compounds in yakju, strains with strong resistance to low temperatures and excellent production of volatile aromatic compounds were screened from indigenous fruits (grape, persimmon, plum, aronia, wild grape) and nuruk in Korea. One Saccharomyces cerevisiae and three non-Saccharomyces strains were finally screened, and yakju was fermented at 15 °C through mono/co-culture. The analysis of volatile aromatic compounds showed that S. cerevisiae W153 produced 1.5 times more isoamyl alcohol than the control strain and reduced the production of 2,3-butanediol by a third. Similarly, a single culture of Pichia kudriavzevii N373 also produced 237.7 mg/L of ethyl acetate, whereas Hanseniaspora vineae G818 produced ~11 times greater levels of 2-phenethyl acetate than the control. Alternatively, Wickerhamomyces anomalus A159 produced 95.88 mg/L of ethyl hexadecanoate. During principal component analysis, we also observed that the co-culture sample exhibited characteristics of both volatile aroma compounds of the single cultured sample of each strain. Our results suggest that yakju with unique properties can be prepared using various non-Saccharomyces strains.