Some applications in the use of compound-specific isotopic analyses (CSIA) for biomarker source elucidation in the marine environment and its potential applications to paleoclimatology are evaluated in the present study. The potential use of the carbon isotope ratios of marine biomarkers as recorders of CO2 levels has been considered. A significant correlation between delta 13C cholesterol of suspended particulates and seawater CO2 concentrations from the south Indian Ocean has been found. delta 13C composition in biomarkers of different functionalities from three photosynthetic organisms has been examined. Small variations within and between biosynthetically related compound classes have been observed in cyanobacteria. In algae, e.g. diatoms and dinoflagellates, significant differences between the average delta 13C composition of fatty acids and sterols were observed (7.5/1000 and 2/1000, respectively). These differences can be attributed to diverse isotope effects associated with different biosynthetic reactions. Isotopic variations among homologues of the same lipid class have also been observed. In diatoms, variations were up to 5/1000 within each class of fatty acids and sterols and in the dinoflagellate species, these variations were lower than 3/1000. These differences, and particularly the intra-specific shifts in delta 13C lipid composition, must be considered for the correct interpretation of changes in delta 13C molecular signatures in the marine environment.