The export of mangrove primary production to adjacent habitats has long been regarded as playing a significant role in estuarine food webs. In the Logan River Estuary, a subtropical estuary situated in the southern part of Moreton Bay in Queensland, Australia, we used the fatty acid markers approach to investigate this export and its contribution to the estuarine food web, compared to other sources. During summer and autumn of 2004, 4 stations were sampled along a salinity gradient. Surface sediment samples were collected, using pre-cut syringes, in the mangrove forest of each station and in the adjacent tidal flats. Individuals of dominant crab species were also collected from the mangrove forests. Seasonal differences in fatty acid compositions of the surface sediments within the mangrove forests and along the adjacent banks were recorded, indicating that organic matter inputs varied between summer and autumn. Results also showed that mangrove production was accumulated at the surface sediments in some parts of the estuary during autumn and consequently was not exported to the tidal flat. The fatty acid composition of crab species present in the mangrove showed obvious differences between the grapsid and the ocypodid crabs collected from the estuary. These differences most likely reflect the distinctive feeding strategies of the crab groups, although there was some indication of species-specific biosynthesis/accumulation of certain polyunsaturated fatty acids. The grapsid of this study, Paraseserma erythodactyla, in addition to being more dependent on mangrove leaves than the ocypodid crabs, is shown to potentially feed on fungal biomass.