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Carbon cycling in coastal sediments was investigated using stable isotopes of carbon and nitrogen and radiocarbon isotope of various compound class fractions from a subsurface sediment section (30–50 cm) of Santa Monica Basin (SMB) and a composite of six surface grab sediments from McMurdo Sound, Antarctica. The range of stable isotope ratios reflects a mixture of terrestrial and marine inputs in the SMB sediments. By contrast, the uniformity of the carbon isotopic signature in the Antarctic sediments is characteristic of a dominantly planktonic contribution. Additional information on sources, particle processing and organic matter preservation was obtained by integrating the stable isotope data with radiocarbon measurements and molecular composition of the same fractions. Inputs of carbon from submarine seeps in coastal sediment are obvious from the relatively older age observed in the aliphatic and aromatic hydrocarbon fractions from the sediments of SMB. On the other hand, eroded sedimentary sequences containing coal could have imparted a non-recent age to the aliphatic and aromatic fractions in the Antarctic sediments. A major biogenic origin is evident from the younger age of most of the Antarctic sediment organic fractions compared to those from SMB. The humic and fulvic acid fractions from both the regions of investigation exhibit relatively young age in the range of 760–1700 BP. In contrast, protokerogen is much older (5470 and 8770 BP, respectively) than the humic and fulvic acids in both the sample locations. This suggests that protokerogen is more likely derived from the selective accumulation and preservation of refractory residues of biological organic components rather than being generated by in situ humiflcation. These results have important implications to the carbon cycling in coastal sediments and in understanding the formation of kerogen.