A popular commercial traditional Filipino rice wine, locally known as tapuy from Banaue and Mountain Province, is made from a natural starter culture called bubod. Bubod is a white, oval, and disc-shaped hardened starch powder that contains a mixed cultures of molds, several yeasts and lactobacilli bacteria which carry out the saccharification and natural fermentation process. The study aimed to isolate, characterize, purify the DNA of the principal yeast in bubod and establish its molecular identity using PCR amplification and DNA sequencing. The native wine yeast was initially propagated on peptone yeast glucose (PYG) agar and broth, isolated and purified by pour plate and streak plate method. The yeast isolate reproduced by unilateral budding and fermented only glucose. Molecular identification of the isolated yeast from Bubod was Pichia kudriavzevii at 78% homology. The morphological characteristics, unilateral budding and ability to ferment solely glucose matched and confirmed the yeast identity.