Forty alcohol yeast strains were isolated from the main mashes (10 strains from each mash) for brewing of 4 different kinds of Korean traditional liquor (3 different types of Yakju and 1 Takju). Thirty-eight out of 40 strains were identified to be the same strain, Saccharomyces boulardii, by the Automated Bacteria, Yeast, and Fungi Identification System (Biolog Co., U.S.A.) based on the metabolic fingerprints. One strain that showed the highest ethanol production among the 38 strains in YPD medium, designated SHY 111, was selected and used for differentiating from other yeast type strains using the polymerase chain reaction (PCR). Amplified DNA, from transcribed internal spacers of SHY 111 chromosomal DNA, was found to be the same in both size and sequence as those of S. cerevisiae KCCM 11215 (formerly S. coreanus) and S. boulardii along with that of S. cerevisiae AB 972, which was used as a type strain for the yeast genome project. However, when PCR was carried out with the intron splice site primer, it resulted in the amplification of the SHY 111-specific DNA fragment which was about 200 bp in size. When PCR was carried out using the primer to test diversity of 40 isolated yeast strains, it was found that the PCR patterns were similar to each other except for the 200 bp bands derived from all the 10 strains from one Yakju, and 2 strains from another Yakju. These results suggest the strain identified as S. boulardii by the Automated Identification System to be a dominant strain for the fermentation of Korean traditional liquors.