The maximum quantum yield of photosystem II (as reflected by variable to maximum chlorophyll a fluorescence, F v /F m ) is regarded as one of the most important photosynthetic parameters. The genetic basis underlying natural variation in F v /F m , which shows low level of variations in plants under non-stress conditions, is not easy to be exploited using the conventional gene cloning approaches. Thus, in order to answer this question, we have followed another strategy: we used genome-wide association study (GWAS) and transgenic analysis in a rice mini-core collection. We report here that four single-nucleotide polymorphisms, located in the promoter region of β-glucosidase 5 (BGlu-5), are associated with observed variation in F v /F m . Indeed, our transgenic analysis showed a good correlation between BGlu-5 and F v /F m . Thus, our work demonstrates the feasibility of using GWAS to study natural variation in F v /F m , suggesting that cis-element polymorphism, affecting the BGlu-5 expression level, may, indirectly, contribute to F v /F m variation in rice through the gibberellin signaling pathway. Further research is needed to understand the mechanism of our novel observation.