Polyploidy (i.e., hybridization between more or less divergent genomes, associated with whole genome duplication) has been shown to result in drastic genome reorganization. Such changes involved major restructuring and epigenetic repatterning, mainly in transposable element (TE) fractions. Polyploidy thus is an adequate model to explore the mechanisms generating genome variation and their impact on evolution. In this chapter, we will review available evidence on the importance of TEs in the short-term and the long-term changes in polyploid genomes. We will argue that the study of polyploid systems not only offers the opportunity to highlight specific mechanisms controlling the activity of TEs but also the evolutionary impact of TE-induced genome reorganization.