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[Objectives] The paper was to explore the correlation between active components of ginseng and community structure of endophytic fungi in ginseng under different cultivation methods. [Methods] Using ginsengs under two main planting patterns in Huanren County, Liaoning Province as the samples, the community structure of endophytic fungi was studied by molecular means, and the chemical components were identified and the content of chemical markers was measured via LC-MS. Moreover, the correlation between medicinal components of ginseng and diversity of endophytic fungal flora was analyzed. [Results] The diversity and active components of endophytic fungi of ginseng were different. The diversity analysis showed that the medicinal components of ginseng were positively correlated with some fungal groups in ginseng. [Conclusions] Artificial intervention in the planting process would affect the endophytic fungi in medicinal materials, and further affect the chemical components of ginseng medicinal materials. [ABSTRACT FROM AUTHOR]