This study was designed to determine the anthocyamn cyanidin-3-glucoside content and antioxidant activity of rice varieties under salinity stress. Two classes of Thai rice lines: cyanic (Riceberry, Kham, and Khamdoisaket) and acyanic (KDML 105, Sinlek, and BC2F7#62-56) were hydroponically grown. Seedlings were grown for 16 days and were supplied with salinity nutrient solution with 0 (control) and 60 mM NaCl for 11 days. The total phenolic content and the antioxidant activity, including 2,2-diphenyl-1-picrylhydrazyl free radical-scavenging, ferric reducing antioxidant power, and lipid peroxidation were also determined by colorimetric assay. Anthocyanin pigment cyanidin-3-glucoside was quantified by high performance liquid chromatography. The results show that salinity stress in Khamdoisaket and KDML 105 cultivare significantly (p < 0.05) increased the total phenolic content, antioxidant activity, and cyanidin-3-glucoside content. Riceberry, Kham, and Sinlek cultivare, showed a moderate increase. The salt tolerant variety, BC2F7#6256, showed only a slight but not significant increase in antioxidant activity and virtually unchanged lipid peroxidation, total phenolic content, and anthocyanin cyanidin-3-glucoside content under salinity stress. These results suggest that the increased total phenolic content, antioxidant activity, and anthocyanin cyanidin-3-glucoside content in rice seedling might be a protection mechanism against salinity stress. BC2F7#62-56 seems to have potential tolerance to salinity stress. This capability could be related to unchanged antioxidant activities, lipid peroxidation, total phenolic content, and anthocyanin cyanidin-3-glucoside content.