Overwhelming evidence suggests that seagrass ecosystems are declining around the world. Pathogens from the genus Labyrinthula have repeatedly been found to cause disease in a variety of seagrass species. For example, the ‘wasting disease’ of Zostera marina has been attributed to Labyrinthula infection. Although poorly characterized taxonomically, species of Labyrinthula are very common in marine ecosystems, virulence of genotypes/phylotypes is known to be variable, and highly virulent species are able to cause ecologically significant diseases of protists, plants and animals. Here, the pathosystem model is applied to host–parasite relationships in seagrass ecosystems. Known physical and biological stressors of seagrass are reviewed. Finally, we make the case that it is time to expand research on this poorly studied microorganism in order to quantify the role of disease in seagrass populations world-wide.