Northeast China is well known for cultivating ginseng ( and ). Ginseng roots are threatened by the infection of the most notorious -like fungi (CLF), which are a complex containing important soilborne pathogens. Although the disease is economically important, little is known about the genetic diversity and population structure of the pathogenic CLF complex. This knowledge will help in developing effective disease management strategies. To conduct this study, diseased ginseng roots were collected from 12 regions representing the main ginseng-growing areas in Northeast China, and CLF were isolated. A total of 169 isolates with CLF anamorph were identified in two species and six species using morphological and molecular methods. Cross pathogenicity tests showed that all species were pathogenic to both and , and most of them had slightly stronger aggressiveness in . The analysis of partial sequences of the gene generated a high level of genetic diversity and geographic differentiation. A total of 132 variable sites were detected in 169 sequences, which formed 20 haplotypes with a haplotype diversity of 0.824. Genetic differentiation was positively correlated with geographic distance. The geographic populations in the range of Changbai Mountain were distinctly discriminated from those in other non-Changbai Mountain populations. No significant genetic differentiation was found between ginseng hosts. -like fungi causing ginseng root diseases are geographically correlated in the genetic distance in Northeast China and should be managed correspondingly.