The Intergovernamental Panel on Climate Change (IPPC) defined a marine heat wave (MHW) as "an event at a particular place and time of the year that is rare and predominately, but not exclusively, defined by a relative threshold; that is, an event rarer than 90th or 99th percentile of a probability density function". MHW has increased frequency in the past century and coastal lagoons as Ria Formosa with interdial pools and shallow subtidal areas drives the water temperatures to rise dramatically in times of hot weather. This changes can significantly affect the physiology and survival of all types of species found in the Ria Formosa, including seagrasses. The objective was to comparatively evaluate the physiological response of two seagrass species, Zostera marina and Cymodocea nodosa, to marine heatwaves.