Seagrass ecosystems are recognised for their role in climate change mitigation, due to their capacity toform organic-rich sediments. The chemical recalcitrance of seagrass organs is one characteristic drivingcarbon storage, but the molecular background of this feature is poorly understood. We assessedmolecular composition changes ofPosidonia australissheaths (SH) and roots plus rhizomes (RR) alonga sediment core, encompassing 3200 cal. yr BP, by means of nuclear magnetic resonance spectroscopy(13C NMR), conventional analytical pyrolysis (Py-GC–MS) and thermally assisted hydrolysis and methy-lation (THM-GC–MS). Significant trends with depth (age) in the composition of both SH and RR remainsofP. australiswere observed from all methods. In general terms, polysaccharides become depleted(degraded) and lignin enriched (selectively preserved) as age increases, and the minor constituents cutin,suberin and condensed tannin are also preferentially depleted during ageing in both fractions. Molecularchanges with ageing were smaller in SH, especially regarding polysaccharides, indicative of a superiorstability compared to RR. The molecular changes observed are most pronounced within the first 75 cmof the record, which reflects the recalcitrance ofP. australisdetritus once it is buried below that depth(corresponding to approximately 700 cal. yr BP). The capacity ofP. australisto act as a long-term carbonsink seems to be mainly related to the resistance of buried lignocellulose materials to decomposition. Theresults on diagenetic effects on the molecular fingerprint of seagrass detritus contribute to our under-standing of carbon sequestration in Blue Carbon ecosystems. Furthermore, data comparison of the meth-ods applied using principal component analysis (PCA) allowed us to identify consistencies, discrepanciesand complementarities.