Abstract: The proteins of male-sterile line, its fertile maintainer line and the hybrid F1 were separated by two dimensional electrophoresis with immobilized gradients as the first dimension and SDS-PAGE as the second, and the high resolution and repeatability 2D maps were obtained. 15 differentially expressed points were identified by MALDI-TOF/MS or LC-MS/MS analyses and protein database searching, and then the subcellular localization and function analyses were performed. The results showed that some proteins involved in material and energy metabolism, transcription and signal transduction etc. were down-regulated or absent in the male-sterile line, It seemed reasonable to infer that the decrease or absence of those proteins in male-sterile might relate to the pollen sterility caused by the mitochondrial insufficient energy.