The study of lithic raw materials recovered from archaeological sites offers relevant data on source catchment areas. Additionally, it can provide first hand information on artefact displacement, interchange networks and it can reflect the way in which the artefacts were employed. In order to characterize geological and archaeological chert samples and with the aim of finding an analytical fingerprint infrared and Raman spectroscopies were used for molecular analysis and X-ray Fluorescence spectrometry for elemental analysis. In this work, different chert samples coming from several localities with geological and archaeological importance from the Basque Country have been collected and analysed. As a consequence, Raman spectroscopy allowed to distinguish between alpha-quartz and moganite in chert samples without organic matter and it is suggested that the ratio of those two components is related to the source of the chert. In addition, the impurities that appear in the samples (CaCO(3), iron oxides and organic matter) can open new features to distinguish the samples and in this way, it would be possible to discuss the use and transport of the lithic artifacts from the sources to the final settlements.