We applied a multivariate analysis to investigate the roles of host and symbiont on the in situ physiological response of genus Madracis holobionts towards light. Across a large depth gradient (5-40 m) and for four Madracis species and three symbiont genotypes, we assessed several variables by measuring chlorophyll a fluorescence, photosynthetic pigment composition, or symbiont population descriptors. Most of the variation is explained by two major photobiological components: light-use efficiency and symbiont cell densities. Two other minor components emphasize photoprotective pathways and light-harvesting properties such as secondary pigments. Statistics highlight the role of irradiance on coral physiology and reveal mechanisms that are either genetically constrained, such as symbiont cell sizes, or environmentally dependent, such as photochemical efficiencies. Other parameters, such as cellular light-harvesting and photoprotective pigment concentrations, are regulated by host, symbiont, and environment. The interaction between host and environment stresses the role of host properties in adjusting the internal environment available for the endosymbionts. Different holobiont strategies, relating to symbiont cell density, vary in their physiological optimization of light-harvesting or photoprotective mechanisms and link to host-species distribution and dominance over the reef slope. Symbiont functional diversity appears to have a significant role but does not explain host vertical distribution patterns per se, highlighting the importance of species-specific morphological and physiological properties of the coral host.