Coral bleaching represents the most serious threat to contemporary coral reefs. In response, focus is being laid on understanding the cellular processes involved in the response of corals to the environmental stresses and the molecular mechanisms that determine the bleaching patterns. In the present study, a component of the cellular stress response such as the expression of the heat shock proteins (Hsps) was analyzed following the coral bleaching event which occurred in the central Red Sea (Saudi Arabia) in 2015. During this event, corals of different species, growth forms and sites showed variable bleaching susceptibility. In particular, we investigated the expression of Hsp70, Hsp60 and Hsp32 in both healthy and bleached colonies belonging to four different coral species (Goniopora lobata, Porites lobata, Seriatopora hystrix and Stylophora pistillata), in order to explore the intra- and inter-specific modulation of these biomarkers as well as the existence of spatial patterns of Hsp expression. In healthy colonies, the level of all the biomarkers was significantly different among the different species, although within each species it remained similar regardless of the distance from the shore. All the coral species showed a significant modulation of the Hsp expression in response to bleaching, whose typology and amplitude were species-specific. In all the species, Hsp70 and Hsp60 showed a coordinated dual expression, which, in response to bleaching resulted in an up-regulation in G. lobata and P. lobata and in a down-regulation in S. hystrix and S. pistillata. Hsp32 was up-regulated in all four species following bleaching, indicative of elevated oxidative stress. Overall, the protein expression profiles of each species contribute to assess the role of Hsps in regulating the susceptibility to thermal stresses of the various coral taxa of the Red Sea.