Marker genes are widely studied and used in plant genetic engineering. To distinguish transformed and untransformed cells and tissues, this review provides a summary of marker genes in terms of classification, working principles, application and problems. Based on biosafety considerations, eight different aspects of marker genes are discussed, including traditional selective marker genes; marker genes related to hormone metabolism, amino acid metabolism, and saccharide metabolism; proteins with detoxifying activity, as well as specific fluorescence proteins, and the knock-out technique of antibiotic marker genes. Marker genes connected with tissue- or organ-specific promoters, the multi-auto- transformation (MAT) vector system and b-glucuronidase as a multifunctional marker gene, as well as the prospects of marker genes are also discussed.