Comparative studies of chloroplast proteome on different developmental stage (seeding, tillering, shooting, booting stage) of leaves have been made in isoplamic allonuclear male-sterile lines Nongda 3237A, Xiaoyan No.6 A and their maintainer lines by 2D-PAGE. The results indicated that no obvious differences were found in chloroplast proteome between Nongda 3237A, Nongda 3237B, Xiaoyan No.6A, Xiaoyan No.6B at different developmental stages of leaves. Differences were found just at booting stage in Xiaoyan No.6A and its maintainer lines. Obvious differences, however, were observed in chloroplast proteome between isoplasmic allonuclear male-sterile lines Nongda 3237A and Xiaoyan No.6A. For instance,2 protein spots (pl5.4/34kDa, pl5.4/32kDa) at seedling stage,6 protein spots (pl5.4/80kDa, pl5.4/65kDa, pl5.4/60kDa, pl5.4/48kDa, pI5.4/40kDa, pI5.4/35kDa) at booting stage were present in Xiaoyan No.6A and absent in Nongda 3237A. pl6.3/18kDa was present at seedling stage in Nongda 3237A and absent in Xiaoyan No. 6A. pI6.8/28kDa protein spot revealed the developmental changes. It was present in leaves at seedling, tillering, shooting stages and absent at flowering stage in Nongda 3237A. No development changes of the protein spot were observed in Xiaoyan No.6A. These experiment results demonstrated that it was possible chloroplast proteome wasn't relative to the cytoplasmic male-sterile characteristics. But nuclear background in male -sterile lines can obviously affect chloroplast protein composition. Distant relative on nuclear-cytoplasmic has larger differences on chloroplast proteome than close relative on nuclear-cytoplasmic in CMS.