Stable isotopes of carbon were used to trace organic and inorganic carbon cycles and biogeochemical processes, especially methanogenesis within different geologic substrates of the Pliocene lignite-bearing Velenje Basin in northern Slovenia. Lithotypes of lignite, coalbed gases, calcified woods (xylites), carbonate-rich sediments, and groundwaters were investigated. Carbon isotope (delta C-13) values of the different lignite lithotypes ranged from -28.1 to -23.0 parts per thousand, with the variability likely a function of the original isotopic heterogeneity of the source plant materials and subsequent biogeochemical processes (i.e. gelification, fusinitization, mineralization of organic matter) during the early stage of biomass accumulation and diagenesis. In the lignite seam, CO2 and CH4 were the major gas components with small amounts of N-2. The carbon isotope values of CO2 (delta C-13(CO2)) and CH4 (delta C-13(CH4)) were highly variable, ranging from -9.7 to 0.6 parts per thousand and -70.5 to -34.2 parts per thousand, respectively. Carbon dioxide is likely sourced from a mixture of in situ microbial activity and external CO2, while CH4 is dominantly sourced from microbial methanogenesis, with possible addition of thermogenic gas from deeper formations, and the influence of microbial oxidation of methane. Calcified xylites enriched with C-13 (delta C-3 values up to 16.7 parts per thousand) indicate that microbial methanogenesis was active during formation of the basin. The delta C-13(DIC) values (from -17.4 to -3.2 parts per thousand) of groundwaters recharging the basin from the Triassic aquifer are consistent with degradation of organic matter and dissolution of dolomite. Groundwaters from the Pliocene sandy and Lithotamnium carbonate aquifers have delta C-13(DIC) values (from -9.1 to 0.2 parts per thousand.) suggestive of degradation of organic matter and enrichment via microbial reduction of CO2. (C) 2011 Elsevier B.V. All rights reserved.