The light microclimate of phototrophic endoliths growing within the scleractinian corals Porites cylindrica and Montipora monasteriata was described by scalar irradiance microprobe measurements within different layers of the coral skeleton. Characterisation of the pigments in individual layers was done by reflectance spectroscopy with fibre-optic radiance microprobes. The spectral measurements showed the presence of an endolithic community largely comprised of the green alga Ostreobium sp. within a 1 to 2 mm thick green band 2 to 6 mm below the coral surface. Additionally, spectral signatures of cyanobacteria and anoxygenic phototrophic bacteria were detected both in the coral tissue-containing top layer and within the skeleton matrix. The light microclimate within the coral skeleton was extremely poor in visible light but enriched in far-red wavelengths. Only a fraction of the incident photosynthetically available radiation (PAR, 400 to 700 nm) penetrated the coral tissue-containing layer, wherein 90 to 99% of the incident irradiance was attenuated due to intense scattering and absorption. Near-infrared radiation (NIR, >700 to 1000 nm) was mainly scattered in the tissue-skeleton matrix and penetrated much deeper into the skeleton. Multiple scattering and light-trapping effects caused high NIR scalar irradiance levels in the topmost layers of the coral. Our data show that the endolithic community in healthy corals is strongly light-limited with respect to PAR, but not with respect to NIR in shallow waters where water absorption of NIR is not limiting. Light limitation of PAR is mainly imposed by the tissue-containing part of the coral, and could thus be alleviated during coral bleaching, resulting in blooming of the phototrophic endoliths.