Posidonia oceanica forms extensive peat-like deposits (mats) in Mediterranean coastal waters, which have a potential as carbon sinks and archives of environmental change. Nonetheless, the organic chemistry of both P. oceanica plant materials, as well as the environmental and diagenetic effects on the composition of its detritus, is poorly understood. We analyzed plant organs of P. oceanica and the coarse organic matter from a mat core spanning 750 yrs using pyrolysis techniques (PY-GC-MS and THM-GC-MS) to improve our understanding of their molecular properties and their preservation upon mat development. It appeared that leaf sheaths, roots and the outer parts of rhizomes were composed predominantly of phenolic constituents based on p-hydroxybenzoic acid (p-HBA), which is atypical for vascular plants, in addition to carbohydrates and lignin. The inner rhizome and leaf blades had a different composition, with predominance of carbohydrates. The seagrass detritus in the mat was composed mainly of p-HBA phenolic material and carbohydrates, confirming earlier studies showing that the coarse detritus in the mat originates largely from Posidonia sheath, root and rhizome debris. The intermolecular arrangement of the p-HBA remains unclear, as they seem to correspond to ester-bound phenols yet their persistence in the mat attributes them a refractory nature. Variations in molecular composition within the mat are probably associated with diagenetic alteration of P. oceanica detritus, such as the decomposition of minor amounts of fatty acids, chlorophyll and syringyl lignin, and selective preservation of p-HBA relative to carbohydrates. This work lays the foundations for a molecular understanding of carbon storage within the mats and the environmental changes recorded therein.