BACKGROUND: Identification and characterization of endophytic yeasts inhabiting the roots of Ulmus parvifolia Jacq. and Quercus salicina Blume require biotechnological and culture-based techniques. METHODS AND RESULTS: Homogenized U. parvifolia and Q. salicina root samples were spread onto four types of agar medium containing ancgtibiotics, L-sorbose, and Triton X-100. In total, 25 yeast strains were isolated and subjected to phylogenetic analysis based on their internal transcribed spacer region sequences. The results revealed that the yeast genera Cyberlindnera (12 isolates) and Cryptococcus (1 isolate) were associated with roots of U. parvifolia; and the genera Rhodotorula (8 isolates), Trichosporon (3 isolates), and Kluyveromyces (1 isolate) were associated with roots of Q. salicina. Additionally, a Kluyveromyces isolate produced a detectable level of bioethanol. The yeast strains reported herein may be used in industrial production of biosurfactants and bioethanol. CONCLUSION: Our findings revealed that the endophytic yeast genera Cyberlindnera and Cryptococcus predominated in roots of U. parvifolia; and the genera Rhodotorula (8 isolates), Trichosporon (3 isolates), and Kluyveromyces (1 isolate) predominated in roots of Q. salicina. Additionally, Kluyveromyces isolates produced a detectable level of bioethanol.