UVB radiation sensitivity among rice cultivars varied widely. The possibility that UV-resistant rice cultivar might exhibit higher cyclobutane pyrimidine dimer (CPD) photorepair ability compared with UV-sensitive one, has been indicated. Here, we show that UVB sensitivity among rice cultivars is tightly linked with CPD photolyase activity by quantitative genetic approach using UV-resistant Sasanishiki (japonica rice cultivar) and UV-sensitive Surjamkhi (indica rice cultivar). Firstly, we confirmed that the CPD photolyase activity in Surjamkhi was significantly lower than that in Sasanishiki. There were two variations at codons 126 and 296 in the deduced amino acid sequence of CPD photolyase between both cultivars, and these mutations affected the CPD photolyase activity. Next, to test whether the alteration of the CPD photolyase causes the difference in UVB sensitivity in rice, QTL analysis for linkage between UVB sensitivity and CPD photolyase with DNA makers developed in flanking region of CPD photolyase gene, using the population derived from a Sasanishiki/Surjamkhi was carried out. There was a peak with LOD score 24.5 at the region located photolyase gene. Thus, these results suggest that the spontaneously occurring mutation in CPD photolyase gene could lead to difference in UVB sensitivity in rice.