Plant–endophytic fungus interactions have been extensively investigated. Most of the symbionts may have helped for host plants. It has also been confirmed that the pathogenic–endophytic lifestyles of some fungi are interchangeable [61] and [62]. These phenomena are caused by many factors, such as environment changes, chemical inducers, and molecular and genetic bases [63] and [64]. Groups of fungal phytopathogens also contain large numbers of endophytic taxa. In this study, isolates PH30409 and PH30412 caused root-rot symptoms in experimental infection through detached healthy roots of P. notoginseng (unpublished data). Interestingly, crude extracts of them showed antagonistic activities against the tested phytopathogens, and more experimental infections to confirm the pathogenicity of Cladosporium sp. for P. notoginseng in plantation are underway. It is also interesting that some species in Alternaria and Fusarium from soil are pathogenic fungi for P. notoginseng, and these genera were dominant groups in the endophytic isolates. In the cultivation soil, Fusarium was the most isolated genus [65]. Endophytes should originate from the environment in which their host plants live. Therefore, these genera have more opportunities to invade and colonize in the tissues, and evolve as endophytes. Their evolution should be investigated in the further studies.