Starch is the most widespread form of energy storage in the plant kingdom. Although many enzymes and related factors have been identified for starch biosynthesis, unknown players remain to be identified given that it is a complicated and sophisticated process. The endosperm of rice (Oryza sativa) has been used for the study of starch synthesis. Here, we report the cloning and characterization of Floury Endosperm6 (FLO6) gene in rice. In flo6 mutant the starch content is decreased and the normal physicochemical features of starch are changed. Significantly, flo6 mutant endosperm cells show obvious defects in the compound granule formation. Map-based cloning showed that FLO6 encodes a protein of unknown function. It harbors an N-terminal transit peptide that ensures its correct localization and functions in the plastid, and a C-terminal CBM48 (carbohydrate-binding module48) domain that binds to starch. Furthermore, FLO6 can interact with isoamylase1 (ISA1) both in vitro and in vivo, while ISA1 does not bind to starch directly. We thus propose that FLO6 may act as a starch-binding protein which involves in starch synthesis and compound granule formation through direct interaction with ISA1 in developing rice seeds. Our data provide a novel insight into the role of proteins with only CBM48 domain in plant species.