AbstractIsotopic studies of coal organic matter are often conducted to gain information about past ecosystems and plant communities e.g. under changing climate conditions. While many studies focused on isotope analysis of bulk coal organic matter or extractable aliphatic hydrocarbons, the polar fraction and compounds that are bound to kerogen and not freely extractable have received less attention. The aim of this study was to provide a systematic comparison and evaluation of information gained from different molecular compounds (n-alkanes, n-carboxylic acids) extracted from Paleozoic coals before and after alkaline hydrolysis. Stable carbon isotope analysis of these compounds were used to evaluate a possible application of extractable and ‘bound’ lipids for paleoenvironmental analyses. Coal samples of different stratigraphic age, low thermal maturity (VRr < 1.02%, mostly VRr < 0.8%) and from different paleogeographic locations were selected to investigate organic matter deposited under different paleoenvironmental and paleoclimatic conditions. Molecular distributions show prominent carbon preference suggesting preservation of biologic signatures in coal organic matter. Permian Gondwana coals show similar n-alkane and n-carboxylic acid distribution which may be related to Glossopteris flora. Molecular distributions of Carboniferous coal from Europe are more variable with unimodal or bimodal patterns and maxima in the short- or long-chain range, reflecting higher diversity of paleovegetation and different contribution from algae or bacteria in limnic and paralic environments. The isotope signals of free as well as bound fatty acids show closer response for different depositional environments, whereas signals of paraffins and bulk organic matter are less variable. However, averaged fatty acid isotope signals in coals from different paleovegetational realms, e.g. Euramerica and Gondwana differed only marginally. Graphical abstract