The applicability of Saccharomycopsis fibuligera CJN1020, Pichia jadinii CJN1287, and Saccharomyces cerevisiae CJN1514 isolated from Korean nuruk, a starter culture, for preparation makgeolli was investigated. These yeasts were suitable for preparation of both white rice makgeolli using a steam method and white rice-brown rice-wheat flour (WBW) makgeolli using a complex method. Upon physicochemical evaluation, there were no differences in the final ethanol concentrations between white rice makgeolli and WBW makgeolli. Differences in final ethanol yields occurred according to yeast species. Final ethanol yields using S. fibuligera and P. jadinii were 16 and 18% using S. cerevisiae. WBW makgeolli samples received higher sensory scores than white rice makgeolli for overall preference. GC/MS analysis revealed higher amounts of aromatic compounds in WBW makgeolli than in white rice makgeolli. The complex method was suitable for preparation of makgeolli using brown rice and wheat flour.