The culture-based study and molecular identification showed that the total fungal diversity was relatively high, and the overwhelming majority belonged to Ascomycota (96.6% of the total number of isolates). Only a single Zygomycota group was obtained. This finding is consistent with a previous study in Cannabis sativa L. . In 12 morphologically distinct groups, Hypocreales (29.2%) and Pleosporales (21.3%) were dominant orders among the endophytic fungi of different tissues of P. notoginseng. This result was similar to the previous studies in many medicinal plants . The endophytic fungi associated with P. notoginseng comprised a number of dominant groups, such as Alternaria, Fusarium, and Penicillium.