We studied the allelopathic effects of barnyard grass (Echinochloa crus-galli (L.) Beauv.) on the morphological and physiological responses of rice accessions. The seedlings of allelopathic rice accession 'PI312777' or a non-allelopathic rice accession 'Lemont' were co-cultured with barnyard grass (BYG) in various ratios in hydroponic culture. In the presence of BYG, the root length, plant height and plant dry weight of rice 'PI312777' were increased with increasing rice: BYG ratios, compared with control of 'PI312777'. On the other hand, these morphological parameters of rice accession 'Lemont' were not changed at the rice: BYG ratios of 4:1 and 2:1, except the root length which was significantly increased at the rice: BYG ratio of 4:1, than control of 'Lemont'. However, these morphological parameters of rice accession 'Lemont' were decreased at the rice: BYG ratio of 1:1, compared with the control of 'Lemont'. Different rice: BYG ratios did not influence the activities of superoxide dismutase, peroxidase, and catalase enzymes in the roots and leaves of 'PI312777'. The activities of these enzymes in the roots and leaves of 'Lemont' were optimum at the rice: BYG ratio of 4:1, after which they decreased with increasing rice: BYG ratios. The photosynthetic parameters of 'PI312777' increased with increasing rice: BYG ratios. However these parameters of 'Lemont' increased only at the rice: BYG ratio of 4:1, after which they decreased with increasing rice: BYG ratios. Three important genes (ribulose-1,5-bisphosphate carboxylase, phosphoenolpyruvate carboxylase, and glycolate oxidase) related to photosynthesis in rice were upregulated in both rice accessions in response to barnyard grass stress. However, gene expression was more upregulated in 'PI312777' than in 'Lemont'. These results suggested that 'PI312777' and 'Lemont' showed distinct responses to barnyard grass stress.