In comparison to some corals, massive Porites spp. is physiologically resilient to environmental assaults and is becoming more abundant on coral reefs. To evaluate the extent to which thick tissues contribute to this physiological resilience, we tested the hypothesis that the Symbiodinium in Porites lutea are phenotypically and genetically homogeneous with regard to their distribution vertically within the tissue, and in their response to temperature. Symbiodinium density, genetic identity, and photophysiology were compared between outer and inner tissues defined as adjacent layers ~2 mm thick and beneath the skeleton surface. Symbiodinium densities were 5-fold greater and their cells contained less chlorophyll a in outer versus inner tissue, but ITS2 sequence identities were genetically uniform between layers. Maximum photochemical efficiency (Fv/Fm) in inner and outer tissue from the top and sides of the corals differed 6%–7%, with Fv/Fm greater in inner versus outer tissue on the top of colonies. On the tops of colonies, the initial slopes of the rETR versus irradiance relationship were not different between tissue layers, although they tended to be less steep for inner tissue. When exposed for 12 h to 28°C, 30°C, or 32°C at ~700 mmol quanta m-2 s-1, there was a trend for Fv/Fm of the Symbiodinium in both tissue layers to be reduced at 32°C. Our results do not conform well to shade acclimatization in inner versus outer tissue of P. lutea, and they imply within-tissue heterogeneity that may be an important determinant of physiological performance in perforate corals.