The effects of chilling stress on chloroplasts at protein and mRNA levels to provide a reference for further investigation on the molecular mechanism of chilling stress in sugarcane was investigated.Sugarcane varieties GT28(strong cold resistant)and ROC22(weak cold resistant)were used as plant materials,and treated under 9 d,15 d and 24 d of chilling stress,respectively.The chloroplast protein was extracted and used for electrophoresis analysis,and expressions of the genes were analysed using real-time PCR.Electrophoresis analysis showed that,for both sugarcane varieties,the relative content of chloroplast protein decreased with increase in chilling time.The protein bands of 39.92,32.95 and 22.87 kDa were down-regulated.Mass spectrometry revealed that they were ATP synthase subunit gamma,oxygen-evolving enhancer protein 1 and chloroplast 23kDa polypeptide of photosystem Ⅱ,and they were encoded by atpC,PsbO and PsbP genes,respectively.Their fragment lengths were 937,996 and 721 bp respectively.The obtained fragment of PsbO gene,in its complete open reading frame,has been registered in the GenBank database with the accession number JQ898540.Real-time PCR analysis showed that chilling stress suppressed the expression of atpC gene,but induced the expressions of PsbO and PsbP genes,which reached a maximum at 15 d.Generally,chilling stress promoted protein degradation,and the protein declined more in ROC22 than that in GT28.Chilling stress suppressed the expression of atpC gene,but induced the expressions of PsbO and PsbP genes in chloroplasts of sugarcane.