LTR (long terminal repeat) RTs (retrotransposons) are almost ubiquitous in eukaryotic genomes. Their abundance and selfish properties make them a major influence in the regulation and evolution of their host genome. Recently, several striking properties of the LTR RTs of fission yeast have been uncovered, affecting important cellular processes such as gene regulation, nuclear architecture and genome integrity. The present review summarizes the current information and puts it in the context of the wider search for understanding the influence of transposable elements on the host genome. 