Abstract: Background and Objective: Anthocyanins have been implicated to offer some protective roles for vegetative and reproductive tissues under abiotic stresses. In this study, the effects of salt stress on physiological responses including anthocyanin accumulation and the expression of anthocyanin biosynthetic genes in seedlings of two cultivars of black glutinous rice (Oryza sativa L.) differing in the levels of salinity tolelance and leaf anthocyanin were investigated. Materials and Methods: Two rice cultivars namely Niewdam Gs. No. 00621 (salt-tolerant, deep purple leaf colour) and KKU-LLR-039 (salt-sensitive, greenish purple leaf color) were grown in a hydroponic culture until 21 days old. Thereafter, they were treated with 0, 75 and 150 mM NaCl for 0, 2, 4, 6 and 8 days. Leaf tissues were collected for physiological determination and expression analysis of anthocyanin biosynthesis genes. Results: The growth parameters, total chlorophyll and chlorophyll fluorescence ratio (Fv/Fm) were progressively reduced while the electrolyte leakage rate increased with increasing NaCl concentrations and the length of time of salinity treatments. For all physiological parameters, the cultivar Niewdam Gs. No. 00621 was less afftected under salt stress. The highest anthocyanin content was attained after 2 and 4 days of salt stress in KKU-LLR-039 and Niewdam Gs. No. 00621, respectively; followed by a reduction in both cultivars until 8 days of salt stress. Real-time PCR analysis showed that the patterns of expression of anthocyanin biosynthesis genes Phenylalanine Ammonia Lyase (PAL), chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS) were related with variations in anthocyanin contents. The maximum expression levels of CHS, DFR and ANS compared to those of non-stressed controls were observed after 2 and 4 days of stress for KKU-LLR-039 and Niewdam Gs. No. 00621, respectively, thereafter the expression dramatically reduced after 6-8 days of stress. The anthocyanin content and relative expression of the four genes was higher in the leaves of Niewdam Gs. No. 00621 than in KKU-LLR-039. Conclusion: Higher accumulation of anthocyanins may be one of the protective physiological traits under salt stress. Therefore, the rice cultivar with deep purple leaf color suffered from less severe cellular damages and lower growth reduction under salt stress compared with the one with less intense anthocyanins.