Marine plants are only incidentally included in conservation efforts for marine biodiversity. Here, for the first time, we apply phylogenetic methods to marine macrophytes (mangroves and seagrass species) to test for gaps in the current conservation network by identifying global diversity hotspots for these plant groups, and assess the degree to which hotspots are represented within the current network of marine protected areas (MPAs). Global. We calculated five metrics of marine plant diversity: phylogenetic diversity, species richness, species endemism, phylogenetic endemism and ‘evolutionary distinctiveness and global endangerment’ (EDGE). Overall, the diversity of marine plants was poorly represented by current MPAs. Different measures of diversity showed spatial mismatch, demonstrating how strategies that maximize one diversity measure may be inefficient at protecting other facets of marine plant biodiversity. However, complementarity analyses revealed that complete representation can be achieved very efficiently with few additional locations. Our study highlights the need for an integrative approach to conserve both the species diversity and phylogenetic diversity of marine plants. While MPAs are a valuable instrument for conserving marine biodiversity, we now face the challenge of increasing coverage to protect other branches of the marine tree of life.