Reef-building corals inhabiting the mesophotic zone (30−150 m) not only survive but thrive in light-limiting environments. Similar to shallow corals, mesophotic corals also exhibit coral fluorescence. Because fluorescent proteins (FPs) absorb high-energy light and emit lower-energy light, FPs could play an important role in mesophotic coral physiology and ecology. For 4 species of the Hawaiian mesophotic reef-building coral Leptoseris (65−125 m), we investigated the abundance of fluorescent morphs, types of FPs, fluorescence emission phenotypes, and the physiological relationship between coral fluorescence and endosymbiotic Symbiodinium (dinoflagellate; Dinophyta). Cyan/green coral fluorescence emission was widespread in mesophotic Leptoseris spp.; more than 70% of corals fluoresced, yet fluorescent and nonfluorescent corals co-occurred at all depths investigated. Coral fluorescence was attributed to 2 proteins, a cyan fluorescent protein (CFP, λex = 424 nm, λem = 490 nm) and a green fluorescent protein (GFP, λex = 478 nm, λem = 502 nm). The type of FP in Leptoseris colonies was correlated with depth; CFP was dominant in corals from shallower depths (65−85 m), GFP was dominant in corals from deeper depths (96−125 m), and CFP and GFP were present in corals from middle depths (86−95 m). Coral FP emission was primarily localized in the coenosarc and/or the oral disc. Symbiodinium from corals with and without fluorescence emission had similar genotypes, abundances, photosynthetic pigments, photosynthetic efficiencies, photosynthetic rates, and chlorophyll excitation spectra. As such, it is unlikely that these FPs play a significant role in enhancing symbiont photosynthesis. The high abundance of fluorescent morphs (>70%) dominating this energetically limited environment may suggest that FPs play an integral and conserved physiological role in corals.