To investigate the impact of heatwaves on the transcriptome of R, decussatus and R philippinarum and the role of seagrass in shaping such impact, a mesocosm experiment was carried out. Juveniles of the two species inhabiting two types of habitat, bare sand and sand with Z. noltei, were exposed to an atmospheric heatwave during diurnal low tide for four consecutive days and subjected to whole transcriptomic analysis.