The precise understanding of diagenetic pathways occurring during fossilization of biomineralized skeletons is of critical importance for various related fields in both paleontology and sedimentology. In particular, this may have fundamental implications in paleoenvironmental studies for interpreting geochemical proxies extracted from these skeletons. The effects of the first diagenetic processes on both mineral and organic compounds present in skeletons of scleractinian corals were investigated in two different coral colonies (Lobophyllia corymbosa and Leptastraea purpurea) by combining mapping of skeletal ultrastructural patterns by SEM and in situ analysis by Raman microspectroscopy. The two elementary ultrastructural features typical of scleractinian corals, the centers of calcification and the sets of aragonite fibers, have been characterized in the uppermost parts (i.e. the "living zone") of both coral colonies. Diagenetic features affecting the skeleton itself and also represented by fibrous diagenetic cements have been analyzed in the oldest basal parts of each colony. All Raman spectra display several vibrational bands typical of aragonite (but no calcite). Additionally, several Raman bands indicate the presence of organic compounds, some of which likely characterize proteinous components, and provide the first in situ chemical record of the skeletal organic matrices. Tentative assignments to CH, CH2, CH3, NH2, CHO, CNC, and SO groups are proposed. In the "living zone," some of these bands are different in the two coral species. In Raman spectra measured in the oldest skeletal parts of both colonies, these bands decrease markedly in number and diversity or even disappear, indicating that significant decay of intraskeletal organic matrices does occur in just a few years. Therefore, early diagenesis in these skeletons results from the interaction between the degradation of organic matrices and the diagenetic processes affecting the skeletal aragonite submicron-size crystals.