Retrotransposons in eucaryon are mobile genetic elements with ubiquitousdistribution,these elements can amplify themselves via RNA intermediates and increase their copy numbers in genome.In high plants,retrotransposon is an important component of genome.Retrotransposons can be divided into five types,the LTR retrotransposons,an important subclass of transposable elements,are well suited for computational identification,as they contain two long terminal repeats (LTRs) and features such as PBS,PPT,GAG and POL open reading frames,TSD.Recent research indicated that methylation of LTR retrotransposon and environments seemed to be affecting the jump of retrotransposons.Retrotransposons could be inhibited by high degree of DNA methylation and activated by environments,which influence the function of surrounding genes.The characteristics of LTR retrotransposons,such as ubiquitous distribution,abundant copy number and insertional polymorphism in plant species,provide an excellent basis for the development of molecular markers,e.g.,RBIP,SSAP,IRAP,REMAP.In this review,we summarize the recent progress about the types and structures of retrotransposons,inhabitation and activation of LTR retrotransposons and their computational identification,molecular marker development.