Abstract The biogeography of host–pathogen interactions shapes disease dynamics by influencing pathogen presence, host susceptibility and environmental factors. This study investigates the genetic diversity of the protist Labyrinthula in eelgrass (Zostera marina) ecosystems, a model for host–pathogen research. Labyrinthula zosterae (Lz), the pathogen responsible for eelgrass wasting disease, causes leaf lesions that lead to necrosis, shoot mortality and habitat loss. We collected eelgrass sample