It is a key of the breeding of allelopathic rice cultivars to evaluate and screen few accessions with allelopathic traits from numerous rice accessions and individual plants. Rice varieties and individual plants with allelopathic traits demonstrated their allelopathic effects by producing and releasing specific secondary metabolites into environment. Therefore, using specific secondary metabolites as markers, the allelopathic potentials of rice varieties and individual plants could be evaluated by HPLC. The allelopathic potentials of 3000 rice accessions and some individual plants of F3 and F4 were evaluated by this method in 1 a. If these accessions and plants were evaluated by the traditional method in the field, it would take more than 10 a, furthermore, the breeding process of allelopathic rice cultivars would be directed and monitored by this method. Isolation and structural identification of specific secondary metabolites was done by LC/MS coupling 1H and 13C NMR. It revealed that allelochemicals of rice tissue were glucosides of resorcinol, flavone and hydroxamic acid, and were not well-known phenolic and fatty acids in previous studies. However, these glucosides could degrade immediately into sugar, phenolic and fatty acids under microbial and acidic medium when they released into the environment.