In order to predict the performance of growth, development and resistance of a citrus diploid cybrid plant between Citrus unshiu Marc. cv. Guoqing No. 1 (G1) and Hirado Buntan pummelo (Citrus grandis (L.) Osbeck) (HBP), the proteomes of leaves from this cybrid and its parents were investigated. First, the diploid cybrid plant (G1 ? HBP) created with its nuclear and chloroplast genomes from HBP and mitochondria genome from G1 was further verified by ploidy and molecular analysis (SSR, CAPS and cp-SSR). Then, 2-DE combined with MALDI-TOF/TOF MS were employed to analyze the variation of proteomes in the cybrid and its parental plants. Significant analysis allowed 90 (P \ 0.05) differentially expressed protein spots between G1 and the cybrid, 20 between HBP and cybrid, and 116 between G1 and HBP. The comparative proteome patterns well validated the genetic background of the cybrid and its parental plants, suggesting that there is a good correlation between genome constitution and proteome expression in this cybrid. Seventy differentially expressed spots were selected for MALDI-TOF/TOF analysis and 25 proteins were identified. The identified proteins were mainly involved in photosynthesis, stress response, anti-oxidative stress and metabolism. Five proteins involved in photosynthesis such as Rubisco and Rubisco activase were significantly up-regulated in the cybrid, indicating the photosynthesis is enhanced in the cybrid. Expression analysis of proteins involved in stress response and anti-oxidative stress suggested that the resistance might be improved while anti-oxidative system exhibited a complex effect in the cybrid. The nitrogen, sulfur, carbon and energy metabolism might also be affected in the cybrid plant.