This work is focused on the chemical characterization of the organic residues preserved in ceramic fragments that are suspected to have been used by the Basque whalers in the period from 16th to 17th Century to store whale oil. The lipid profiling along with the identification of biomolecular markers, makes possible to obtain information on the contents of the vessels and on the transformations undergone by the organic substances during the burial process. To achieve this goal, two complementary analytical techniques, High-Performance Liquid Chromatography - Electrospray Ionization - Quadrupole Time-of-Flight Mass Spectrometry (HPLC-ESI-QToF) and Gas Chromatography-Mass Spectrometry (GC–MS), were used not only to study the archaeological materials but also fresh whale oil products used as reference materials with the aim to detect potential diagnostic biomarkers. HPLC-ESI-QToF was used to identify triacylglycerols (TAGs) and study their distribution in the various samples, whereas GC–MS after suitable derivatization provided the fatty acid (FA) profile together with the detection of degradation compounds (dicarboxylic and dihydroxy fatty acids) and biomarkers related to marine commodities (isoprenoid acids). Samples of blubber from 5 different whale species belonging to the genus Balaenoptera (fin, sei and minke whale), Megaptera (Humpback whale) and Phocoena (harbour porpoise) were used as reference materials together with a sample of whale oil of unknown origin. The chemical results confirm the archaeological data regarding the vessels use as containers to store whale oil and indicate the whales from Balaenoptera genus as the most probable source of the oil.