Retrotransposons are mobile genetic elements that make up a large fraction of most eukaryotic genomes. They are particularly abundant in plants, as a principal component of nuclear DNA. Retrotransposons can be divided into two main categories, those with long terminal repeats (LTRs), such as retroviruses and LTR retrotransposons (Ty1-copia type and Ty3-gypsy type), and those lacking such repeats, as long interspersed nuclear elements (LINE type) and short interspersed nuclear elements (SINE type). Most retrotransposons sequences normally show inactive, but some could express under biotic and abiotic stress. Differences observed in plant genomes can be attributed to retroelement amplification leading to genome expansion. So retrotransposons contribute greatly to the genetic diversity and genome size variability of plants. Up to date, active retrotransposons have been introduced into a few plant species. These elements have been used as a powerful tool for studying plant gene functions and expression. In this paper, the progress of plant retrotransposons for recent years is systematically reviewed from the following aspects: structure, charateristics, activation, effection of plant genome and application of fuctional genomics.