The definition, basic characteristics and fundamental mechanism of allelopathy are illustrated simply. On the basis of correlation with biodiversity theory the diversity of species, allelo-chemicals of allelopathic effect and their released pathways were summarized. Then the possible effects of allelopathy on biodiversity of species, genetic diversity and community ecology, co-evolution, soil habitation, ecological function and biological invasion in biodiversity of ecosystem were discussed concretely. An important idea on the combination between the utilization and management of allelopathy and the biodiversity protection was proposed. Meanwhile an essential study on the relationship and mutual influence mechanism between allelopathy and biodiversity, especially, its service function and values in ecosystem, should be considered a new approach for biological scholars, which will establish a academic basis for protection biology and chemical ecology.