The Raman and surface enhanced Raman scattering (SERS) spectra of a black dyed silk sample (BDS) were registered. The spectral analysis was performed on the basis of Raman and SERS spectral data of isolated samples of Bombyx mori silk fibroin, its motif peptide component (GAGAGS) and the synthetic reactive black 5 dye (RB5). The macro FT-Raman spectrum of the silk sample is consistent with a silk II-Cp crystalline fraction of Bombyx mori silk fibroin; the SERS spectrum is highly consistent with conformational modifications of the fibroin due to the interactions with the Ag nanoparticles. The GAGAGS peptide sequence dominates the Raman spectrum of the silk. The SERS spectrum of the peptide suggests a random coil conformation imposed by the surface interaction; the serine residue in the new conformation is exposed to the surface. Quantum chemical calculations for a model of the GAGAGS–Ag surface predict a nearly extended conformation at the Ag surface. The Raman spectrum of the dye was analysed, and a complete band assignment was proposed; it was not possible to propose a preferential orientation or organization of the molecule on the metal surface. Quantum chemical calculations for a model of the dye interacting with a silver surface predict a rather coplanar orientation of the RB5 on the Ag metal surface. The Raman spectrum of the BDS sample is dominated by signals from the dye; the general spectral behaviour indicates that the dye mainly interacts with the silk through the sulphone (–SO2–) and sulphonate (–SO2–O–) groups. Besides the presence of dye signals, mainly ascribed to the sulphone and sulphonate bands, the SERS spectrum of the BDS sample also displays bands belonging to the amino acids alanine, glycine, serine and particularly tyrosine. Copyright © 2013 John Wiley & Sons, Ltd.