Recent micro-analytical studies of coral skeletons have led to the discovery that the effects of biology on the skeletal chemical and isotopic composition are not uniform over the skeleton. The aim of the present work was to provide histological observations of the coral tissue at the interface with the skeleton, using Stylophora pistillata as a model, and to discuss these observations in the context of skeletal ultra-structural organization and composition. Several important observations are reported: (1) At all scales of observation, there was a precise morphological correspondence between the tissues and the skeleton. The morphological features of the calicoblastic ectoderm correspond exactly to the shape of individual crystal fiber bundles in the underlying skeleton, indicating that the calicoblastic cell layer is in direct physical contact with the skeletal surface. This is consistent with the previously observed chemical and isotopic composition of the ultra-structural components in the skeleton. (2) The distribution and density of desmocyte cells, which anchor the calicoblastic ectoderm to the skeletal surface, vary spatially and temporally during skeletal growth. (3) The tissue above the coenosteal spines lack endoderm and consists only of ectodermal cell-layers separated by mesoglea. These findings have important implications for models of vital effects in coral skeletal chemistry and isotope composition.