The nature and distribution of organic matter in geological cherts of archaeological use can serve to estimate the sources and origins of some remains of lithic industry. For example, organic and biomarker analysis can provide information to allow a deeper insight into source catchment areas, artefact displacement or the way in which the artefacts were employed. In this work, soluble (bitumen) and insoluble (kerogen) organic matter were isolated from several chert samples with different depositional history and analysed by means of gas chromatography–mass spectrometry (GC–MS) and spectroscopic techniques such as infrared and Raman spectroscopy. Chemometric treatment of the results allowed observation of differences between organic matter content on the basis of the depositional setting of the cherts. Samples with a continental deposition seemed to preserve more organic matter with little alteration. The hydrocarbon profiles of these samples were dominated by high molecular weight n-alkanes, alkylcyclohexanes and isoprenoid groups which allowed distinguishing them from the rest of the analysed samples.