The paper deals with the ancient timber structures of the Royal Palace of Naples (1600), which represent unique study cases of complex timber roofs and beam floors. The structural identification of some of them, in particular the roofing structures of the Royal apartments, has been achieved through the following subsequent levels of investigation: 1) in situ surveys, for getting both geometrical and mechanical features, through visual inspection combined with Non Destructive techniques, aimed at detecting defects and degradations; 2) FEM analyses on approximated structural models, for providing the stress distribution and deformation state of members, thus evidencing the critical parts of the structures and the residual strength. The selection and design of appropriate retrofitting interventions, where necessary, have been enabled by the acquired deepen knowledge of the timber structural systems.