Analysis of the jaws of the Humboldt squid (Dosidicus gigas) and Nautilus belauensis using mass spectrometric techniques revealed a chitin-protein composition, confirmed by analysis of chitin and amino acid model compounds. Analysis of comparable fossil material from several cephalopod taxa (Placenticeras, Nanaimoteuthis jeletzkyi, Anagaudryceras limatum and Hoploscaphites) from Upper Cretaceous (Campanian and Maastrichtian) localities from North America and Japan revealed no compounds from the chitin-protein biopolymer complex but showed the presence of aromatic compounds, including alkyl benzene derivatives, alkyl phenols, naphthalenes, and phenanthrene. An n-alkyl component, ranging in chain length up to C24, was also detected. There was no evidence of the presence of these compounds in the host sediment. Cleavage of ester bonds in the fossil macromolecules (including fossils with both predominantly aromatic and aliphatic compounds) using thermally assisted methylation (THM) revealed a carboxylic acid distribution from C6 to C18. Additionally, methyl ketones were detected in the fossils, in which the n-alkyl (aliphatic) component was significant. Methyl ketones (alkan-2-ones) have been reported in fossil algae and kerogen and are indicative of ether functional groups in macromolecules, which are probably crosslinked via oxidative reticulation. Thus, the aliphatic component is likely derived from in situ incorporation and polymerisation of labile lipid precursors, in part crosslinked via ether and ester bonds. This is the first demonstration of ether linkages and of oxidative crosslinking in animal fossils, suggesting that such a process may be important in the long term preservation of both animal- and plant-derived organic matter.