Marine diatoms are promising feedstock for biofuel industries as a source of hydrocarbons and fatty acids. In the present study, eleven marine diatom isolates from the west coast of India were analysed for hydrocarbons and lipids. The comparative analyses indicated that Psammodictyon panduriforme (MACC 35), a diatom isolate from the water samples collected from 1000 m depth, with a hydrocarbon yield of 37.27 mg g−1 L−1 and 2.1 % of the total biomass of 0.56 gL−1 was a promising species followed by Biddulphia sp. (MACC 6) with hydrocarbon yield of 25.4 mg g−1 L−1 and 1.3 % of the total biomass of 0.48 g L−1. Hydrocarbon analyses by gas chromatography with high resolution mass spectrometry (GCMS) showed that the long chain hydrocarbons found in the majority of the marine diatoms were undecane 4,7 dimethyl, hexadecane, octadecane,3-ethyl-5-(2-ethyl-butyl), tetradecane, tetracosane, eicosane-2 methyl, heptacosaneand hexacosane. The fatty acid profile showed the presence of stearic acid, 9-octadecenoic acid, myristic acid, palmitic acid, and arachidic acid with excellent biodiesel properties. Hydrocarbons of high fuel quality can be produced by optimizing hydrocarbon production in the potent marine diatom Psammodictyon panduriforme and catalytic cracking of long chain hydrocarbons to short chain alkanes with high octane ratings.