Fatty acid compositions of the leaves of six species of mangroves were studied to ascertain their use as biomarkers for determining the fate of mangrove organic matter in the habitat and as taxonomic tool. Mangrove leaves were collected from three locations in the western Pacific Ocean: Moreton Bay (MB) (Australia), Hong Kong (China) and Okinawa (Japan). In MB, samples were collected from two sites separated by 15km: Logan River Estuary (LRE) and Jabiru Island. In addition, along the LRE, leaves were collected from five stations at ∼2–3km apart. Results show that the analysis of the entire fatty acid profiles of the mangrove leaves is a promising taxonomic tool as the profiles of most species were sufficiently different to be separated in an non-metric multidimensional scaling plot. In addition, geographically separated populations of the same species could also be identified by their fatty acid profiles. In most cases, two non-ubiquitous groups of fatty acids dominated in the mangrove leaves: the polyunsaturated 18:2ω6 and 18:3ω3 and the long chain fatty acids (≥24:0). With respect to the relative contributions of these fatty acids, three groups of species were identified, in which one or both groups of fatty acids may potentially be used as markers of the mangrove organic matter in the estuarine environment.