Mangroves are amongst the most productive ecosystems (2500 mg C d-1) on Earth; are intertidal tropical ecosystems covering up to 60–75% of the coast, that strongly impact the global carbon budget. Coastal residents rely on mangroves to sustain their traditional cultures, food production, medicines, fishery, where as muddy/sandy sediments of mangroves provide home to a variety of invertebrates. In addition, mangroves protect coastal inhabitants from natural calamities like tsunami and cyclones. Organic matter (OM) from both autochthonous and allochthonous sources accumulates in estuarine systems. These organic compounds derive from coastal wetlands and/or salt marsh, mangrove forests, benthic vegetation, riverine sediments, and freshwater and marine phytoplankton. While mangrove ecosystems are a source of organic carbon and nutrients to adjacent coastal systems on one hand they are also a sedimentary sink for organic carbon. The aim of this study is to assess the utility of a combined approach using natural product biomarkers (hydrocarbons, sterols, and triterpenoids) to differentiate terrestrial and algal derived OM inputs to sediments of the Pichavaram mangrove estuarine complex in south-eastern India. The five sediment core samples were collected, extracted with various organic solvents, and the extracts analyzed on a GCMS. In general, the mangrove sediments extracts have higher concentration of different biomarkers compared to the extracts from the estuarine area. The higher abundance and unimodal distribution of the long-chain n-alkanes (mainly C25, C27, C29; and predominance of phytosterols (β-sitosterol and stigmasterol) and triterpenoids namely taraxerol, β-amyrin, germanicol, and lupeol indicate the presence of higher plant matter preserved in these sediments.