Stable carbon isotope ratios for aliphatic biomarkers were measured on 34 Late Palaeozoic coals. Compound specific isotope analysis allowed the determination of delta C-13 values of individual organic compounds such as chlorophyll side-chain derived substances (pristane and phytane), leaf wax constituents (n-alkanes), or bacteria related compounds (hopanoids). Pristane and phytane can be regarded as excellent isotopic tracer molecules to ascertain isotope fractionation during primary production of organic matter by land plants in the Late Palaeozoic. Compared to the organic carbon isotope values for total terrestrial organic carbon, partly different isotope shifts and temporal trends are discernible for these isoprenoids. Such differences in carbon isotope ratios of total terrestrial organic matter and isoprenoids indicate that both isotope data sets record different bio-geochemical information. Since phytolderived isoprenoids are directly linked to the primary production of organic matter, their carbon isotopic properties seem to be most appropriate for the reconstruction of ecological systems and climate in the Palaeozoic. Interestingly, isotopic values of isoprenoids and hopanoids were not significantly affected by maturity and maceral composition of the coals. However, differences between the isotopic composition of total organic matter and of phytane (Delta delta C-13 values) and differences between the isotopic composition of total organic matter and of hopane seem to correlate with provenance of the samples, i.e. samples from different basins show different values. Hence, variations in different types of organic biomass might be successfully traced by the isotopic properties of characteristic molecular fossils in Palaeozoic coals. This might become an appropriate approach for future palaeoenvironmental, palaeoclimatic and palaeogeographical studies. In conclusion, the present study clearly demonstrates that molecular and carbon isotopic analyses of terrestrial organic matter, range in resolution from bulk to compound specific analyses, and it allows for the reconstruction of ecological and climatic conditions in the Late Palaeozoic. (C) 2012 Elsevier B.V. All rights reserved.