Great changes in the study of plant genetic breeding had been brought about by the development of biotechnology,and the application of DNA molecular marker technique is one of the most significant changes.Genetic breeding is an important base for the development of flower plant industry and also is one of the most active branches in technical innovation.The application of molecular marker in the study of flower plants genetic breeding such as construction of molecular genetic map,analysis of relationship,location of ornamental characters and marker assisted selection is described in this paper.