The conventional geochemical view holds that the chitin and structural protein are not preserved in ancient fossils because they are readily degradable through microbial chitinolysis and proteolysis. Here we show a molecular signature of a relict chitin-protein complex preserved in a Pennsylvanian (310 Ma) scorpion cuticle and a Silurian (417 Ma) eurypterid cuticle via analysis with carbon, nitrogen, and oxygen X-ray absorption near edge structure (XANES) spectromicroscopy. High-resolution X-ray microscopy reveals the complex laminar variation in major biomolecule concentration across modern cuticle; XANES spectra highlight the presence of the characteristic functional groups of the chitin-protein complex. Modification of this complex is evident via changes in organic functional groups. Both fossil cuticles contain considerable aliphatic carbon relative to modern cuticle. However, the concentration of vestigial chitin-protein complex is high, 59% and 53% in the fossil scorpion and eurypterid, respectively. Preservation of a high-nitrogen-content chitin-protein residue in organic arthropod cuticle likely depends on condensation of cuticle-derived fatty acids onto a structurally modified chitin-protein molecular scaffold, thus preserving the remnant chitin-protein complex and cuticle from degradation by microorganisms.