Abstract The chemical characterisation of waterlogged archaeological wood is of paramount importance in terms of understanding not only the degradation processes of wood in artistic and archaeological objects but also the development of consolidation and conservation procedures. The two different types of archaeological waterlogged wood were characterized using several analytical techniques. The analytical protocol consists in using PY/GC/MS with in situ derivatisation with hexamethyldisilazane, GC/MS of the extractives, 1H, 13C and 31P NMR analysis, and GPC. The main results showed that one of the ancient samples was a gymnosperm wood from the Pinaceae family, whereas the other type of wood was an angiosperm. Lignin from the angiosperm was oxidised in a benzylic position of β-O-4 to give oxo functional groups, in primary alcohol moiety to give carboxylic groups. In addition, the formation of a new intermonomeric bond 5-O-4 was observed.