This study assessed the nutrient acquisition strategies of two scleractinian corals, Montastraea cavernosa and Agaricia spp., collected from shallow (depths less than 20 m) and mesophotic (depths of 30–150 m) habitats. The composition of biomarker sterols, bulk stable carbon and nitrogen isotope values, and compound specific stable isotope analysis (CSIA) of the sterols were analyzed to assess changes in feeding strategies of the corals. Both species acquired nutrients by heterotrophic feeding and translocation from symbionts. Colonies of M. cavernosa acquired photosynthetic nutrients in shallow and mesophotic habitats, and the relative sterol (and phytosterol) composition did not change with depth. CSIA evidence suggests that photosynthesis slowed with increasing depth. Colonies of Agaricia spp. used heterotrophic feeding throughout their depth range and acquired some photosynthetic nutrients in shallow habitats and few in mesophotic habitats. Both corals, Agaricia spp. and M. cavernosa, may be able to take advantage of deep reef refugia to maintain populations in a changing ocean by using distinct nutrient acquisition strategies.