Tropospheric ozone (O ₃) significantly reduces rice yield. Koshihikari, a leading Japanese rice cultivar, has been recognized as an O ₃ tolerant cultivar; however, the mechanisms underlying its high O ₃ tolerance remain unknown. Therefore, we aimed to elucidate the genetic and physiological mechanisms underlying high O ₃ tolerance in Koshihikari. A series of chamber experiments were conducted to examine photosynthesis, growth, yield-related traits, and gene expression profiles under chronic O ₃ conditions in Koshihikari and Takanari, with contrasting O ₃ tolerance. Koshihikari showed no reduction in unhulled-grain weights due to higher total dry weight under chronic O ₃ conditions, whereas Takanari showed significantly lower grain weights. The high O ₃ tolerance in Koshihikari was attributed to its highly stable photosynthetic performance and increased biomass allocation to its leaf blades. RNA-seq and gene co-expression network analyses revealed that the genes involved in photosynthesis and carbohydrate metabolism are associated with contrasting O ₃ tolerance. OsRbcS3, encoding the RuBisCO small subunit, showed contrasting expression profiles between the two cultivars. In Koshihikari, OsRbcS3 was identified as a hub gene candidate in the gene co-expression network, which was highly correlated with photosynthetic performance. These results suggest that OsRbcS3 plays a key role in the genetic mechanisms underlying the high O ₃ tolerance of Koshihikari.