Abstract: It was reported that it was the deletion of the last two exons from nad7 gene of a subunit of complex I in the mitochondrial respiratory chain that led to tobacco CMS.The gene differences between CMS type and wild type tobaccos were analyzed by bioinformatics at different structure levels of coding protein.The results showed that the deletion of the last two exons from nad7 gene led to the lack of the structural domain of ubiquinone oxidoreductase(NADH) in coding protein,and the absence of NADH structural domain might be a key factor influencing the integrity of complex I in mitochondrial respiratory chain and one of the fundamental causes led to CMS of tobacco.