A brown hull 6 (bh6) mutant of rice was isolated from an EMS-induced IR64 mutant bank. The brown pigments start to accumulate in the hulls after heading and reach a maximum level in mature seeds. The 1000-grain weight and panicle length of bh6 significantly decreased while other agronomic traits including plant height, number of productive panicles per plant, number of filled grains per panicle and seed-setting rate were largely similar to those of the wild-type IR64. Analysis of pigment contents indicated that the levels of total flavonoids and anthocyanin in bh6 were significantly increased. The brown hull phenotype was controlled by a single recessive gene on the long arm of chromosome 9. Sequencing analysis indicated that a single base substitution (G-A) at position 1013 was detected in the candidate gene (LOC_Os09g12150) encoding an F-box domain containing protein. Functional complementation using the wild-type allele could rescue the mutation. The mutation, designated as OsFBX310^bh6, is a new allele of OsFBX310 functioning as an inhibitor of brown hull. Isolation of OsFBX310^bh6 provides useful experimental materials and would facilitate the studies on mechanism of flavonoid metabolism in monocot plants.