Allelopathic rice cultivar PI312777 (PI) and non-allelopathic rice cultivar Lemont (Le) were mixed with barnyard grass (Echinochloa crus-galli L., BYG) at various ratios (rice:weed ratios of 4:1, 2:1, and 1:1) in hydroponic cultures. The expression of four genes, i.e. phenylalanine ammonia-lyase (PAL), cinnamate- 4-hydroxylase (C4H), ferulic acid 5-hydroxylase (F5H), and caffeic acid O-methyltransferases (COMT), which are involved in the biosynthesis of the phenolic compounds in rice, were evaluated by a quan-titative real-time polymerase chain reaction (qRT-PCR). The contents of phenolic compounds in leaves, roots, and culture solutions of the two rice cultivars were determined using high performance liquid chromatography (HPLC). The results showed that all of the four genes were up-regulated in leaves and roots of the allelopathic rice PI at all rice:weed ratios. However, three of the four genes, C4H, F5H, and COMT, were down-regulated in the leaves and roots of the non-allelopathic rice Le. The degree to which PAL was up-regulated in leaves and roots was much higher in PI than in Le. The contents of phenolic compounds in PI leaves, roots, and culture solutions were higher than that in Le leaves, roots, and cul-ture solutions. The higher expression of the genes involved in the phenylpropanoid metabolism and the higher contents of phenolic compounds in PI are consistent with the higher inhibitory rates of PI on BYG. These results indicate that the PAL gene in PI is more sensitive to BYG stress than in Le, and barnyard grass up regulates the biosynthesis of phenolic compound in allelopathic rice.