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The sources of organic matter in three typical mangrove systems of Cochin estuary were assessed for the first time with help of sediment bulk parameters and fatty acid biomarkers. The C/N and δ13C analysis showed intermediate values to that of autochthonous and terrestrial inputs of organic matter, signaling to a mixed origin. The biochemical composition of sedimentary organic matter revealed a dominance of lipids over proteins and carbohydrates, indicating the nutritive or energetic value as well as the freshness of organic matter in all the systems. Fatty acids ranging from C8 to C24 were identified in the study. C20:5n-3 was one of the major fatty acids at station 1, indicating significant benthic phytoplankton contribution. The zooplankton biomarkers C20:1 and C24:1 were also present in appreciable levels, suggesting the tidal influx. Principal fatty acids at station 2 were the zooplankton biomarkers C20:1 and C24:1 implying significant estuarine contribution through tidal influx. The major fatty acids at station 3 were diatom marker C20:5n-3 and the higher plant marker C24:0. Dominant fatty acids in mangrove leaves; C18:2n-6 and C18:3n-3 were also present at station 3. The low contributions of C20:1 and C24:1 confirms the limited tidal exchange at this station. Presence of significant amount polyunsaturated fatty acids in the mangrove sediments confirms the freshness of organic matter. Thus, fatty acid biomarker study of the three mangrove systems of Cochin estuary could substantiate the bulk parameter approaches effectively; distinguishing the multiple sources of the organic matter and the observed spatial variations. [ABSTRACT FROM AUTHOR]