The transfer of fatty acid (FA) biomarkers was assessed by an experimental food chain comprising three trophic levels: leaves of the mangrove Avicennia marina, the grapsid crab Parasesarma erythodactyla, and the blue swimmer crab Portunus pelagicus. FA compositions for each trophic level were investigated through a feeding/starving regime designed to reveal the transfer of FAs along the food chain. Comparison of the FA profiles of the mangrove leaves, the tissues and faecal material of P. erythodactyla suggests that the crab, contrary to previous studies, lacks the necessary enzymes to incorporate some FAs in its diet. Long chain FAs were egested while polyunsaturated acids seemed to be efficiently assimilated. The polyunsaturated FAs 18:2?6 and 18:3?3 were identified as useful biomarkers of the mangrove leaves for tracing their transfer to the higher trophic levels. The contribution of these markers to the FA profiles of the crabs was investigated and it was found that both 18:2?6 and 18:3?3 could be successfully traced across the first trophic transfer. However, only 18:3?3 demonstrated a clear second transfer into the tissues of P. pelagicus. Multivariate analysis of the FA profiles of the study organisms was found to be a potentially useful tool for demonstrating differences in diet within a species and also what FAs, and therefore dietary items, are responsible for those differences. MDS analysis of the FA profiles of faecal material from P. erythodactyla showed that this species provides an important ecological link in estuarine systems by providing a substrate for the colonisation of bacteria.