Marketable probiotic supplements widely used bacterial strains i.e Lactobacilli​ and Bifidobacteria. Another probiotic was recently developed from yeast. Saccharomyces boularldii​ as probiotic yeast that is used in many countries as both a preventive and therapeutic agent for diarrhea and other GI disorders caused by the administration of antimicrobial agents. This research was isolated yeast from tapai, an Indonesian fermented food from steamed cassava. Four tapai were collected from Jember and Bondowoso Regency, East Java-Indonesia. Screening process of yeast was based on their survival in artificial gastric acid on pH 2.0. These yeast strains were cultured in MEA and identified their phenotype and genotype characteristics. Molecular profile using PCR-fingerprinting technique as well as identified sequence homology which compared in the GenBank database using BLASTN and the phylogenetic tree construction also identified. There were two yeasts that have survival on pH 2.0 of artificial gastric acid i.e SUL and SM isolate. The SUL colony was isolated from tapai merk Sumber Madu with morphological characteristics i.e form wrinkled colonies, no contain of pseudo mycelium, the white surface of a colony and round shape of cells. While the SM colony was isolated from tapai merk Sari Madu with morphological characteristics i.e thin wide morphological form colony, no pseudo mycelium, the white turbid surface of colony and oval cell shape. The SUL isolate is more survive (82%) than SM isolate (79%) on pH 2.0 of artificial gastric acid. Genotypic identification resulted that SUL isolate as Kodamaea ohmeri and SM isolate as Pichia kudriavzevii.