Surface‐enhanced Raman spectroscopy (SERS) was used for the identification of natural organic dyes belonging to indigoid and anthraquinone classes in archeological samples, and good agreement with the corresponding reference commercial materials was found. Special attention was paid to the well‐known problem of anomalous bands that arise sometimes in the SERS spectra on colloids: as suggested in the literature, this problem could be reduced by the use of poly‐L‐lysine and ascorbic acid as aggregating agents, but we observed that also the addition first of the analyte and subsequently of suitable electrolytes to the colloid in an inverted order compared to the most widely used method can be of help in limiting the intensity of such spurious bands. This procedure allowed us to obtain, for the first time, the SERS spectra of both modern and ancient Tyrian purple and to solve a specific problem observed in the analysis of archeological wool samples dyed with madder lake, i.e. the competition in the SERS response between the dye and other compounds possibly deriving from the degradation of the peptide chain during the hydrolysis treatment during the extraction of the dye from the wool fiber. Copyright © 2009 John Wiley & Sons, Ltd.