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Anthropogenic activities are driving significant changes in coastal ecological environments, increasingly spotlighting microorganisms associated with seagrass bed ecosystems. Labyrinthula is primarily recognized as a saprophytic protist associated with marine detritus, and it also acts as an opportunistic pathogen affecting marine algae, terrestrial plants and mollusks, especially in coastal environments. The genus plays a key role in the decomposition of marine detritus, facilitated by its interactions with diatoms and through the utilization of a diverse array of carbohydrate-active enzymes to decompose seagrass cell walls. However, human activities have significantly influenced the prevalence and severity of seagrass wasting disease (SWD) through factors such as climate warming, increased salinity and ocean acidification. The rise in temperature and salinity, exacerbated by human-induced climate change, has been shown to increase the susceptibility of seagrass to Labyrinthula, highlighting the adaptability of pathogen to environmental stressors. Moreover, the role of seagrass in regulating pathogen load and their immune response to Labyrinthula underscore the complex dynamics within these marine ecosystems. Importantly, the genotype diversity of seagrass hosts, environmental stress factors and the presence of marine organisms such as oysters, can influence the interaction mechanisms between seagrass and Labyrinthula. Besides, these organisms have the potential to both mitigate and facilitate pathogen transmission. The complexity of these interactions and their impacts driven by human activities calls for the development of comprehensive multi-factor models to better understand and manage the conservation and restoration of seagrass beds.