Selectable marker genes encoding antibiotic and herbicide are widely used in transgenic plants and have a potential risk to the environment and human health. Currently, there are three kinds of strategies to improve security in using marker genes in transgenic plants: One approach is to develop the use of uncontested biosafety marker genes, the second is to use transgenic plants-removed selectable marker genes and the third is the use of non-selective marker gene transformation system. In this review, each of the strategy principles and problems are highlighted. Moreover, the perspectives are discussed to improve the safety of selectable marker genes in transgenic plants.