Abstract Panax notoginseng is a highly valuable herb, but root rot disease severely impairs its development and decreases the yield and quality of roots. In this study, a fungal isolate (3A‐2‐2) was obtained from P. notoginseng seedlings with root rot symptoms and was identified as Plectosphaerella plurivora based on morphological characteristics and molecular analysis. The fungal isolate 3A‐2‐2 could cause root rot disease and be re‐isolated, fulfilling Koch's postulates. This is the first study to report on root rot disease caused by P. plurivora on P. notoginseng in China.