Seagrasses provide the foundation of one of the most highly biodiverse, yet vulnerable, coastal marine ecosystems globally. They arose in three independent lineages from their freshwater ancestors some 100 million years ago and are the only fully submerged, marine flowering plants. Moving to such a radically different environment is a rare evolutionary event and definitely not easy. How did they do it? New reference quality genomes provide important clues with relevance to their conservation and biotechnological application.