Abstract Transposable elements (TEs), which are DNA segments moving within genomes, play a major role in gene and genome evolution of eukaryotes. Plant transposable elements are classified into two major groups: class Ⅰelements or retrotransposons and class Ⅱelements or DNA transposons. Retrotransposons are divided into two principal groups, the long terminal repeat (LTR) and the non-LTR retrotransposons, while DNA transposons are divided into three types, the autonomous elements, non-autonomous elements and miniature inverted-repeat transposable elements (MITEs). The molecular markers based on plant TEs，including sequence-specific amplification polymorphism (S-SAP), MITE display, transposon display (TD), inter-MITE polymorphism (IMP), inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and retrotransposon-based insertion polymorphism (RBIP), were developed. In this review, the principles and applications of above-mentioned markers in genetic biodiversity and phylogeny analyses, gene mapping, and cultivar certification, were summarized.
