By using the tissue isolation method, a total of 80 endophytic fungal strains were isolated from the roots, stems, and leaves of Eucommia ulmoides. Of these, 72 strains that belonged to 13 genera were identified based on their morphological characteristics. The results showed that the Alternaria, Fusarium, and Phoma spp. are the dominant endophytic fungal population found on E. ulmoides, and they comprise 52.78% of the 72 strains. Roots are the most preferred location for most endophytic fungal strains.