Zostera marina is an important ecological seagrass to elucidate the molecular genetic basis of adaptation to environmental stresses. However, transcriptional level mechanisms of salinity tolerance and light quality in seagrasses have scarcely been studied to data. Hence, there is interest in using the halophilic and temperate seagrass Zostera marina to evaluated stress tolerance and adaptation of multiple intertidal stressors such as light reduction, inorganic carbon, temperature and short-term salinity fluctuation.