Three different lithotypes (xylitic, gelified and matrix) of Pliocene lignite from the Velenje Basin, Slovenia, were investigated to establish the variations of biomarker compositions in solvent extracts and the stable isotope (carbon and nitrogen) compositions of bulk material. From the biomarker results, the xylitic lithotype almost exclusively originates from gymnosperms (conifers such as Taxodiaceae), as indicated by the very high contents of sesquiterpenoids and diterpenoids but very low abundances of n-alkanes and non-hopanoid triterpenoids. The relative proportion of gymnosperms to angiosperms in the paleomire is reflected by the ratio of diterpenoids to the sum of diterpenoids and non-hopanoid triterpenoids (Di-/(Di-+Tri-terpenoids)), which is close to 1 (av. 0.99) in the xylitic lithotype. The predominance of diterpenoids from conifers in the xylitic lithotype is associated with high C/N ratios and intermediate total sulfur (TS). The very low abundance of hop-17(21)-ene and the absence of further hopanoids in the xylitic lithotype indicate a restricted influence of bacterial degradation under relatively dry conditions in the paleomire. The matrix lithotype also originated preferentially from gymnosperms under dry depositional conditions, as indicated by the high Di-/(Di-+Tri-terpenoids) ratio (0.95), low amounts of hopanoids and low TS content. The gelified lithotype is characterized by a high content of n-alkanes and wide variation of the Di-/(Di-+Tri-terpenoids) ratio (0.13–0.88), indicating a fluctuating contribution of angiosperms to the plant community in the paleomire during formation of this lithotype. In addition, the high abundance of hop-17(21)-ene and TS in the gelified lithotype compared with the other two lithotypes suggests the effect of bacterial activity under relatively wet/humid conditions during formation of the gelified lithotype, which is also supported by the considerable content of mid-chain n-alkanes. The high correlation between the δ13C and δ15N values (R2 = 0.68) indicates that the stable carbon and nitrogen isotope composition in the Velenje lignites were probably influenced by the same factors (e.g. precursor plants and/or microbial activity). The stable carbon isotopic values (av. −25.44‰) and nitrogen isotopic values (av. 2.15‰) of the xylitic lithotype are higher than those of the gelified lithotype (av. δ13C = −27.48‰, δ15N = 1.37‰) and the matrix lithotype (av. δ13C = −27.09‰, δ15N = 1.10‰). The relatively high correlation between the diterpenoid content and both δ13C and δ15N values suggests that the stable carbon and nitrogen isotopic composition of the three lithotypes might reflect the composition of the original plant material in the paleomire. The dominance of conifers as precursor plants in the xylitic lithotype might be the main reason for the higher δ13C values and probably also the higher δ15N values. The relatively higher δ15N values in the xylitic lithotype than in the other types could be explained by the high amount of decay-resistant xylem and low mineral (e.g. clay) content in the xylitic lithotype. The slightly lower δ13C but higher δ15N values in the gelified lithotype than in the matrix lithotype can be explained by variation of parent plant materials and the influence of bacterial activity. •Different lithotypes (xylitic, gelified and matrix) of Pliocene lignite from the Velenje Basin, Slovenia, were analyzed for biomarkers and stable isotope (C and N) compositions.•The ratio of diterpenoids/(diterpenoids + triterpenoids) reflects the relative proportions of gymnosperms and angiosperms.•Xylitic and matrix lithotypes originate from gymnosperms, while gelified lithotypes are characterized by a fluctuating contribution of angiosperms.•The highest δ13C and δ15N values were measured in xylitic lithotype samples.•The δ13C and δ15N composition is preferentially influenced by the composition of the precursor plants community.