Transposable elements (TEs) are major contributors to the size of plant genomes. For a long time, TEs had a very negative connotation being primarily considered as "parasites" or "junk DNA". In recent years, this view has started to change: Even though TEs can damage genes present in the host genome, they also contribute to stress response and played a key role in crop domestication. Here, we discuss the molecular mechanisms involved in taming TEs, how TEs link the genome and epigenome to the environment, their contribution to gene structure and expression and finally discuss how TE could be used for crop breeding.