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Goldenseal (Hydrastis canadensis L., Ranunculaceae) is a popular medicinal plant and has been listed in Appendix II of the Convention on International Trade in Endangered Species (CITES). The herbaceous perennial is distributed in North America under deciduous forest canopies throughout much of the south and eastern seaboard north into Canada. The rhizome, rootlets and root hairs produce medicinally active alkaloids. Although berberine, one of the Hydrastis alkaloids, has shown anti-fungal activity, the influence of Hydrastis alkaloids on the plant rhizosphere fungal ecology has not been investigated. While a Fusarium spp. was previously isolated from H. canadensis, this is the first report of a F. oxysporum endophyte isolated from Hydrastis root tissue. The findings suggest that the Hydrastis root extract appears to provide selective advantage for the endophytic isolate and influences the fungal ecology associated with its root system. The analysis should shed some light on the debate over whether the quality of botanical medicine produced by plants grown in stable microbial soil populations found in native settings is superior to medicine made by plants from cultivated fields.