This work was conducted to study a new separation and evaluation approach for the chemical fingerprinting of petroleum biomarkers in biota samples. The final aim of this work was to study the correlation between the observed effects in the shore habitats (mussels and limpets) and one pollution source: the oil spill of the Prestige tanker. The method combined a clean-up step of the biota extracts (mussels and limpets), the retention-time locking of the gas chromatographic set up, and the multivariate data analysis of the chromatograms. For clean-up, solid-phase extraction and gel permeation chromatography were compared, and 5g Florisil cartridges assured the lack of interfering compounds in the last extracts. In order to assure reproducible retention times and to avoid the realignment of the chromatograms, the retention-time locking feature of our gas chromatography-mass spectrometry (GC-MS) set up was used. Finally, in the case of multivariate analysis, the GC-MS chromatograms were treated, essentially by derivatization and by normalization, and all the chromatograms at m/z 191 (terpenes), m/z 217-218 (steranes and diasteranes) and m/z 231 (triaromatic steranes) were treated by means of principal component analysis. Furthermore, slightly different four oil samples from the Prestige oil spill were analyzed following the Nordtest method, and the GC-MS chromatograms were considered as the reference chemical fingerprints of the sources. In this sense, the correlation between the studied samples, including sediments and biota samples, and the source candidate was completed by means of a supervised pattern recognition method. As a result, the method proposed in this work was useful to identify the Prestige oil spill as the source of many of the analyzed samples.