The nuclear-encoded light-harvesting chlorophyll a/b-binding proteins (LHCPs) are specifically translocated from the stroma into the thylakoid membrane through the chloroplast signal recognition particle (cpSRP) pathway. The cpSRP is composed of a cpSRP43 protein and a cpSRP54 protein, and it forms a soluble transit complex with LHCP in the chloroplast stroma. Here, we identified the YGL9 gene that is predicted to encode the probable rice cpSRP43 protein from a rice yellow-green leaf mutant. A phylogenetic tree showed that an important conserved protein family, cpSRP43, is present in almost all green photosynthetic organisms such as higher plants and green algae. Sequence analysis showed that YGL9 comprises a chloroplast transit peptide, three chromodomains and four ankyrin repeats, and the chromodomains and ankyrin repeats are probably involved in protein-protein interactions. Subcellular localization showed that YGL9 is localized in the chloroplast. Expression pattern analysis indicated that YGL9 is mainly expressed in green leaf sheaths and leaves. Quantitative real-time PCR analysis showed that the expression levels of genes associated with pigment metabolism, chloroplast development and photosynthesis were distinctly affected in the ygl9 mutant. These results indicated that YGL9 is possibly involved in pigment metabolism, chloroplast development and photosynthesis in rice.