Molecular lignin analyses have become a powerful quantitative approach for estimating flux and fate of vascular plant organic matter in coastal and marine environments. The use of a specific molecular biomarker requires detailed knowledge of its decomposition rates relative to the associated organic matter and its structural diagenetic changes. To gain insight into the poorly known processes of anaerobic lignin diagenesis, molecular analyses were performed in the sulphate-reducing sediment of a North-Brazilian mangrove. Organic matter in samples representing different diagenetic stages, i.e. fresh litter, a sediment core and percolating water, was characterised by alkaline CuO oxidation for lignin composition, element (C, N) and stable carbon isotope analyses. Based on these results and on a balance model, long-term in situ decomposition rates of lignin in sulphate-reducing sediments were estimated for the first time. The half-life (T1/2) of lignin derived from mangrove leaf litter (mainly Rhizophora mangle) was ~150 yrs in the upper 1.5 m of the sediment. Associated organic carbon from leaf tissue was depleted to ~75% within weeks, followed by a slow mineralisation in the sediment (T1/2~300 yrs). Unlike the known pathways of lignin diagenesis, even highly degraded lignin did not show any alterations of the propyl or methoxyl side chains, as evident from stable acid to aldehyde ratios and the proportion of methoxylated phenols (vanillyl and syringyl phenols). Aromatic ring cleavage is probably the principal mechanism for lignin decay in the studied environment. Cinnamyl phenols were highly abundant in mangrove leaves and rapidly depleted during early diagenesis. Thus, the cinnamyl to vanillyl ratio could be used as a tracer for early diagenesis even under the sulphate-reducing conditions. Syringyl phenols were removed from dissolved organic matter in interstitial water probably by sorption onto the sediment. Suspended organic matter in a mangrove creek showed a different lignin signature than its source, namely sedimentary organic matter or mangrove litter, with clear evidence for propyl side chain oxidation. This was probably due to erosion of aerated thin sediment surface layers during mangrove inundation. Although particulate and dissolved organic matter in the mangrove creek have a common source, their compositional patterns were different due to different pathways of release, degradation and transport to the creek.