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Allelochemicals play an important role in biological control of plant pathogens and diseases. Weed Ageratum conyzoides L. and food crop Oryza sativa L. can produce and release many kinds of allelochemicals participating in their defense against pathogens. The essential oil from A. conyzoides has been found to have significant negative effects on several plant pathogens. In the A. conyzoides intercropped citrus orchard, A. conyzoides released allelopathic flavones and agreatochromene into the soil to reduce the populations of soil pathogenic fungi Phytophthora citrophthora, Pythium aphanidermatum and Fusarium solani . Further research revealed that ageratochromene underwent a reversible transformation in the soils, that is, ageratochromene released from A. conyzoides plants was transformed into its dimers, and the dimers can be remonomerized in the soils. The reversible transformation between ageratochromene and its dimers in the A. conyzoides intercropped citrus orchard soil can be an important mechanism maintaining bioactive allelochemicals at an effective concentration, thus, sustaining the inhibition of pathogenic fungi in soil. Many kinds of allelochemicals in rice were identified. Among them, alkylresorcinols, flavone and cyclohexenone had high antifungal activities on Pyricularia oryzae and Rhizoctonia solani . Furthermore, these antifungal allelochemicals formed by rice can be triggered by a large number of abiotic and biotic factors. Antifungal allelochemicals from rice mainly involved two types of diterpenes and flavones, including momilactones A and B, oryzalexins A-F and S, phytocassanes A-E and sakuranetin. These compounds help rice establishing its own pathogen defense mechanism. However, it remains obscure which allelochemicals in rice are predominantly involved in defense mechanisms against the pathogens. Therefore, further clarification of the resistance mechanism and multiple functions of these compounds on rice are warranted.