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Grey mould, caused by Botrytis cinerea, is an increasingly destructive disease of ginseng (Panax ginseng) in China. However, the extent of variation in the morphological characteristics of fungal colonies, genetic background and pathogenicity of different strains of this pathogen remains unknown. In this study, we isolated and identified 102 isolates of B. cinerea from ginseng. Among these, the sclerotial phenotype was dominant, followed by the mycelial and conidial phenotypes, with the proportion of each phenotype in the pathogen population showing no obvious variance across three provinces. Isolates were separated into three groups with differing pathogenicity, based on the diameter of the lesions they caused in pathogenicity tests; moderate-pathogenicity isolates were dominant, followed by strong- and weak-pathogenicity isolates. Variation was observed in the pathogenicity of isolates from three provinces. The Nei's genetic diversity index and the Shannon's information index of isolates from Jilin province was highest, followed by those from Liaoning, while isolates from Heilongjiang displayed the lowest genetic diversity. Furthermore, most of the genetic variance was found within the geographically defined B. cinerea populations; the low-genetic variance among populations was probably counteracted by gene flow. Results from this study provide a base understanding of genetic and pathogenic variation in B. cinerea populations from the main ginseng-growing regions of China, which will be helpful for further research and control of grey mould of ginseng. [ABSTRACT FROM AUTHOR]