The light-limited environment of tropical coral reefs has not been intensively studied due to technical limitations. Studying this vast part of the coral reef is paramount to understanding the ecological and physiological significance of coral–algae symbiosis and defining the boundaries imposed on its bathymetric distribution by the underwater light field. In the present study we describe morphological changes in colonies of the coral Stylophora pistillata and track changes in its carbon sources (autotrophic/heterotrophic behavior) along its full bathymetric distribution. The growth form of hermatypic corals must compromise between an optimal light-trapping surface facilitating photosynthesis and other structures and/or mechanisms that enhance exploitation of nutrient-rich sources such as zooplankton. That architectural modulation is constrained within the species-specific structural and biological characteristics. We found that the profusely branched S. pistillata colonies shift between subspherical morphology at high-light environments to a planar structure at depth. The stable carbon isotopic composition (δ13C) of the host coral tissue changed from a value of –15‰ in shallow water to –23‰ at the deep reef. The latter value indicates either a carbon source with a stable isotope composition equal or below –23‰ or, alternatively, internal carbon cycling between host and algae that involves isotopic fractionation (ε). The δ13C values showed significant correlation to morphological traits, but contradicting trends were found within the traits. A clear shift to heterotrophy was not apparent, which, therefore, suggests that the internal cycling and Rubisco activity are the dominant processes determining isotopic composition.