Deciphering the biomolecular composition of archaeological organic materials can contribute to understand the function of an object or the status of the buried person, and more generally to increase our knowledge on ancient civilizations. The determination of the organic substances composing the sample is based on identifying biomarkers, which is commonly carried out by gas chromatography-mass spectrometry (GC-MS). Here high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) was used, along with GC-MS and infrared spectroscopy, to investigate the organic compounds of embalming material of Egyptian crocodile mummies. FTICR MS was evidenced to provide complementary information with some advantages compared to GC-MS, such as an easier sample preparation. Moreover, although GC-MS allowed identifying 109 different compounds, FTICR MS enabled to assign up to 7000 molecular formulae and to detect higher-mass compounds. Some of the molecular assignments were putatively attributed with biomarkers, which suggested the use of pine resin, beeswax, and vegetal and animal fat, which was confirmed by GC-MS and FTICR MS-MS, for the pine resin. Furthermore, the FTICR MS molecular fingerprint obtained for the archaeological samples was compared with those of modern pine resin, which allowed assessing specie oxidation due the ageing and/or heating process. Consequently, FTICR MS can be regarded as a way to quickly achieve the biomolecular fingerprint of organic residues from archaeological materials and to assess the state of degradation of the sample.