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Panax quinquefolium (American ginseng) is a perennial understory herb that has been widely used as a medicinal plant in China and other countries. Autotoxicity has been reported to be one of the major problems hindering the consecutive cultivation of American ginseng. However, the potential autotoxic compounds produced by the root of American ginseng are less well known. Here, we report the isolation and characterization of five groups of autotoxic compounds from aqueous extracts of the fibrous roots of American ginseng. Ether extracts of the water-soluble compounds were further analyzed and separated into seven fractions. Among them, the most autotoxic fraction (Fraction V) was subjected to GC/MS analysis, and 44 compounds were identified. Based on literature information, 14 individual compounds were selected and their autotoxic effects on seedling growth were further tested. The results revealed that, of these 14 compounds, 9 phenolic compounds significantly reduced the growth of seedlings in a concentration-dependent manner, while 5 aliphatic compounds showed modest inhibition at all three concentrations tested. Furthermore, we verified the existence of the autotoxic compounds in the plow layer soil of commercially cultivated American ginseng fields, and the concentration of these compounds as determined by HPLC analysis was in line with the concentration determined to be bioactive. Taken together, our study established a functional link between the compounds produced by American ginseng and their autotoxic effects. [ABSTRACT FROM AUTHOR]