Grana are thylakoid structures that are observed in land plants and in which photosystem II (PSII) and light-harvesting complex II proteins (LHCIIs) accumulates. We isolated two Arabidopsis mutants, reduced induction of non-photochemical quenching (riq1 and riq2), in which stacking of grana was enhanced. The curvature thylakoid 1a (curt1a) mutant was previously shown to lack the grana structure. In riq1 curt1a, the grana were enlarged with more stacking; furthermore, the thylakoids were abnormally stacked and aggregated in riq2 curt1a. Despite having the opposite phenotype in their thylakoid structures, riq1, riq2, and curt1a showed a similar defect in the level of non-photochemical quenching of chlorophyll fluorescence (NPQ). In riq curt1a double mutants, NPQ induction was more severely affected than in single mutants. In riq mutants, state transitions were inhibited and the PSII antennae were smaller than in the wild type. The riq defects did not affect NPQ induction in the chlorophyll b-less mutant, suggesting that RIQ proteins are involved in LHCIIs dynamics. RIQ1 and RIQ2 are paralogous and encode uncharacterized grana thylakoid proteins. RIQ1 is required for RIQ2 accumulation. The wild-type level of RIQ2 did not complement the NPQ and thylakoid phenotypes in riq1. Despite the high level of identity of the sequence, the functions of RIQ1 and RIQ2 were not redundant. RIQ proteins may link the grana structure and dynamics of LHCIIs.