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Panax  ginseng  rusty root rot caused by the  Ilyonectria  species complex is a devastating disease, and it is one of the main factors contributing to the difficulty in continual cropping. Rusty root rot occurs in all ginseng fields, but little is known about the taxonomy of the fungal pathogen complex, especially  Ilyonectria  and  Ilyonectria -like species. Rusty root rot samples were collected from commercial ginseng cultivation areas of China, and the pathogens were isolated and purified as single spores. Based on the combination analysis of multiple loci (rDNA-ITS,  TUB ,  HIS3 ,  TEF ,  ACT , LSU,  RPB1 ,  RPB2 , and SSU) and morphological characteristics, the pathogens causing ginseng rusty root rot were determined. Fungal isolates were obtained from infected roots in 56 locations within main cultivation areas in China. A total of 766 strains were identified as  Ilyonectria ,  Ilyonectria -like and  Rhexocercosporidium  species, including  I. robusta  (55.0%),  I. communis  (21.7%),  I. mors-panacis  (10.9%),  I. pseudodestructans  (2.0%),  I. changbaiensis  (1.3%),  I. qitaiheensis  (1.3%),  Neonectria obtusispora  (2.0%),  Dactylonectria torresensis  (0.5%),  D.  sp. (0.5%), and  R. panacis  (1.5%), and four novel species,  Thelonectria ginsengicola  (1.0%),  T. jixiensis  (1.0%),  T. mulanensis  (0.8%) and  T. fusongensis  (0.5%), with a total of 14 species. As the pathogen present in the highest proportion,  I. robusta  was the most prevalent and damaging species, unlike the pathogens reported previously. All of the examined strains were proven to cause ginseng rusty root rot. Our results indicate that the taxonomy of the fungal complex associated with ginseng rusty root rot includes  Ilyonectria ,  Ilyonectria -like genera ( Dactylonectria ,  Neonectria , and  Thelonectria ) and  Rhexocercosporidium .

Multi-Locus Phylogeny and Taxonomy of the Fungal Complex Associated With Rusty Root Rot of Panax ginseng in China