Abstract Recent works have paved the way for an understanding of the scale at which environmental signals might be recorded in coral skeletons. In this paper, the resulting structural and chemical insights are exemplified by a Goniastrea corallite. The bulk of the coral skeleton consists of fibrous aragonite, which in turn is constructed by sequential growth of micrometre thick layers, oriented parallel to the local growth direction. These growth layers consist of nanograins (50–100 nm) of aragonite that appear to be crystallized in close association with a matrix, conceivably proteoglycans, which seem to coat individual nanograins. These observations contradict the traditional notion that coral fibre consists of ‘a single crystal of orthorhombic aragonite’. Additionally, the ultrastructural observations provide us with criteria to assess early diagenetic effects. Some Lower Norian corals from South Anatolia (Turkey) display extremely well-preserved mineralogy and structures. They have also preserved the organic components of their skeletons from which it has been demonstrated, through a study of the Nitrogen isotopic composition, that photosynthesis was involved in the metabolism of these early Scleractinia. But even in these remarkably preserved corals, we find evidence for diagenetic changes at the nanometre scale, concerning both the amount of organic matrices and the appearance of the aragonitic nano-granular units. Such micro-structural observations call for caution when interpreting isotopic effects in the fossil coral record.