ABSTRACTTo examine the role of rhodoxanthin in long‐term acclimation to low temperatures, we monitored seasonal changes in pigment composition, photosynthesis, chlorophyll fluorescence and the level of ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) in needles of wild‐type and mutant forms of Cryptomeria japonica. In winter, rhodoxanthin accumulated in sun‐exposed needles of wild‐type plants, but not in those of the mutant. The level of chlorophyll decreased in both types of plant in winter. In contrast, the level of the xanthophyll cycle pool increased in both cases. The level of the pool in the mutant was twice that in the wild type in winter, on a Chl basis, even though the levels in both were similar in summer. The synthesis of rhodoxanthin might be triggered by photo‐inhibitory conditions, as suggested by the sustained elevated levels of zeaxanthin (Z) and antheraxanthin (A). In the wild type and the mutant, the quantum yield of CO2 fixation (φ), the photosynthetic capacity, the photochemical efficiency of photosystem II (PSII), the photochemical quenching and the level of Rubisco in summer were similar. However, all these values for the wild type were higher than those for the mutant in winter. The non‐photochemical quenching (NPQ) in the mutant in winter increased rapidly even under low light conditions due to the high sustained levels of Z and A. In contrast, in the wild type, the conversion of Z via A to rhodoxanthin prevented the rapid increase in NPQ to maintain the relatively high level of φ. These findings suggest that rhodoxanthin might play an important photoprotective role in long‐term acclimation to cold. The dynamic regulation of the amount of rhodoxanthin relative to the level of the xanthophyll cycle pool might act to maintain an appropriate balance between light absorption, photosynthesis and the thermal dissipation of energy due to excess absorbed light in winter.