Bark represents a unique microbial habitat. Revealing the interactions among bark-associated microbes is important for understanding their diversity, stability, and function, and how core microbiome influences the health and production of the host plant. We used amplicon sequencing of bark from the medicinal plant Eucommia ulmoides collected across nine distinct biogeographical regions in China, and comprehensively analyzed the diversity, rare biosphere and core taxa of bark fungi. The co-occurrence network results showed significant differences in the compositions of core mycobiota in E. ulmoides bark between the nine regions. Ecological factors (e.g., temperature and rainfall) were crucial determinants of differences in the unique core mycobiota of E. ulmoides from different regions. The metacommunity-scale network indicated that Cladosporium, Alternaria, and Teratosphaeria were core fungal taxa of E. ulmoides bark. Moreover, some core fungal taxa included rare taxa in particular local communities which, despite their relatively low abundance, may play a significant role in the community structure of E. ulmoides bark.