Onion is a representative cross-pollinated vegetable with obvious heterosis. Cytoplasmic male sterility（CMS）is used to produce hybrid onion seed. It takes 4-8 years of crossing and scoring of progeny phenotypes to identify the sterility-related genotype from an uncharacterized population. The development of molecular marker for cytoplasm male sterility-related genes can improve selection efficiency for maintainer line and be helpful to reveal mechanism of male sterility. This paper introduced several types of onion cytoplasm male sterility and reviewed the progress made in studying molecular marker of cytoplasm and nucleus genes. It also discussed the present status and problems existing in molecular marker technology and prospected its future of application.