Start codon targeted polymorphism (SCoT) is a novel gene-targeted marker that could achieve tightly linked target gene and follow the tracks of the traits properly. As a new kind of marker, it has been widely used in diverse plant species. In this paper, we summarized the principles and the characteristics of SCoT, as well as the primer design and the optimization of SCoT-PCR system. Its applications, such as genetic diversity and phylogenetic relationship analysis, germplasm identification and fingerprinting, gene expression profiling, and genetic linkage mapping, were also reviewed. Besides, the potential problems and the future prospects of SCoT marker were further discussed.