A study on the bulk distributions and molecular structures of n-alkanes and polycyclic aromatic hydrocarbons (PAH) in organic matter of the sediments from the Bay of Bengal and the Eastern and Central Indian Basins was undertaken. The former two regions represent areas characterised by “normal” sedimentation while the third one mainly represents a region of “active tectonism”. Content of the hydrocarbons in the sediments of “normal” sedimentation ranges between 4.6 and 10.5 μg/g and aromatic hydrocarbons ranges between 0 and 0.38 μg/g. n-Alkanes in the sediments of the northern deep part of the Bay of Bengal consist mostly of long-chain structures (total C25–C33 up to 70%) with a high carbon preference index (CPI=3.01–3.43), indicating a large contribution of organic matter from terrigenous sources. The sediments from the Eastern Indian Basin have n-alkane distributions in which the long-chain components did not exceed 52.5% and the CPI was 1.7–1.90, indicating that the hydrocarbons are mostly derived from marine sources. Sharp increases of hydrocarbons are found in the vicinity of the tectonically active region of the Central Indian Basin, particularly in the sediments collected from the fracture zone. The total concentration of hydrocarbons increase to 170 μg/g and the aromatic hydrocarbons fraction to 156.3 μg/g. The proportion of short-chain n-alkanes increases up to 70%, CPI decreases to 0.76–1.12, and high concentrations of n-C16 (16–40%) occur, all of which are absent in the other samples. The molecular content of PAH includes the unsubstituted individual structures: biphenyl, fluorene, pyrene, perylene, benzo(ghi)perylene, and the groups of homologues of naphthalene, benzofluorene, phenanthrene and chrysene. The association of the PAH and composition of paraffin hydrocarbons in the surficial sediments of deformation zone indicate that these are the resultant products of hydrothermal processes. It is, therefore, suggested that the association and composition of the hydrocarbons in sediments can be utilised as a paleoceanographic parameter to decipher the history of tectonism of an area.