During tidal exposure, intertidal seagrass is susceptible to extreme radiation doses, desiccation, thermal stress and excess light leading to membrane and protein degradation. Plants have developed various mechanisms in heat stress adaptation including induction of heat shock proteins (HSPs). Under elevated temperature, production of reactive oxygen species (ROS) also increase and plants must activate their antioxidant defense and protect themselves from heat stress. Here we explore from a molecular perspective the ability of Thalassia hemprichii to activate heat stress response mechanism. Expression of several antioxidant genes (Mn-Sod, Apx, and Cat) and some heat shock protein genes (Hsp70, Hsp81, and sHsp-cp) were observed. The qPCR approach was adapted to understanding the molecular mechanisms of physiological performance from gene expression studies. These finding reported that Mn-Sod, Apx, Cat, Hsp70 and Hsp81 genes were significantly overexpressed as a result of heat stress. However, sHsp-cp was down-regulated.