Suaeda japonica Makino is an annual hydrohalophyte belonging to Chenopodiaceae and inhabits salt marshes in Ariake tidal flats, Japan. One of the distinct traits of S. japonica is the change of the leaf color from green to red-purple and red at different growth stages in response to environmental conditions. The red leaf coloration is due to the accumulation of betacyanin. Although betacyanin biosynthesis is induced by stress conditions, the physiological functions of betacyanin have not been fully elucidated. In the present study, we surveyed the effects of betacyanin on the photosynthetic rate, chlorophyll fluorescence, oxidative stress tolerance based on chlorophyll degradation. Betacyanin accumulated in the epidermal tissues and upper palisade mesophyll. The light intensity transmitted to the betacyanin solution decreased with the increase in the betacyanin content. The betacyanin level varied significantly in leaves, and was negatively correlated to the chlorophyll content. The rate of photosynthetic oxygen evolution, on a leaf area basis, decreased with the accumulation of betacyanin, but on a chlorophyll basis, the rate was higher in the green-red leaves containing some amounts of betacyanin. Betacyanin showed a free radical DPPH (1,1-diphenyl-2-picrylhydrazyl) scavenging capacity, and it prevented chlorophyll bleaching caused by the hydroxyl radical. In red leaves treated with paraquat, a superoxide anion inducer, the degree of chlorophyll degradation caused by oxidative stress was alleviated. The value of non-photochemical quenching (qN), a parameter of chlorophyll fluorescence, was higher and that of photochemical quenching (qP) was lower in red leaves than in green leaves. These results indicated that betacyanin acts as a filter for the light intensity transmitted into the leaf tissues to reduce reactive oxygen species (ROS) generation, and it also acts as a ROS scavenger under stress conditions. Betacyanin may prevent photo-oxidation and photo-inhibition in S. japonica under the harsh environmental conditions prevailing in salt marshes.