Horizontal gene transfer is widespread in prokaryotes, but in multicellular eukaryotes these cases mainly involved in the transposon horizontal transfer. A large number of genome sequencing showed that transposons are an important component of eukaryotic genomes. The most important characteristic of transposon distinguishing from genes is able to mobile and amplify in the host genome, which make them more prone to horizontal transfer. Horizontal transfer is an important way which would allow the element to evade a seemingly inevitable vertical extinction in its original host lineage resulting from genetic drift, natural selection or mutational inactivation. In addition, horizontal transposon transfer in eukaryotic genomes has been a major force propelling genomic variation and biological innovation. Here，this paper would comprehensively summary the methods of identifying horizontal transposon transfer, the transfer mechanisms of transposons, the transfer bias and its contribution in the origin of new genes. Finally，we also discusses the urgency, necessity and importance of studying eukaryotic horizontal transposon transfer from the new perspective of the whole-genome wide.