A set of 39 pale lignite and dark lignite samples, obtained from a profile of the Pliocene Jinsuo lignite basin, Yunnan Province, China, were analyzed using coal petrology and biomarkers to determine whether changes in the depositional environment and/or vegetation caused the color changes ultimately observed in the lignites. A comprehensive analysis of all the data obtained revealed significant differences in the petrological and geo-chemical composition of the two lignite types. The pale lignites are characterized by a higher abundance of the liptinite group compared with the dark lignites. The composition of liptinites is dominated by bituminite (mineral-bituminous groundmass) and sporinite, along with a relatively low abundance of the huminite group. This indicates a higher degree of oxidation in the drier, more elevated peatland environments during deposition of the pale lignites. The low values of the tissue preservation index (TPI), vegetation index (VI), and gelification index (GI) in the pale lignites suggest a relatively high decomposition rate of plant materials under dry/aerobic conditions. In contrast, the dark lignites have a very high proportion of huminite dominated by ulminite, along with a low content of liptinite and inertinite macerals, which suggests the prevalence of wet/anaerobic conditions in the peat-forming mire. The high values of TPI, VI, and GI in the dark layers suggest better preservation of organic matter during deposition under anaerobic conditions, and more wet/humid climatic conditions, when compared with the pale lignites. With respect to the biomarker composition, the high concentrations of long-chain (C-27-C-31) n-alkanes in both pale and dark lignites are typical characteristics for the predominance of higher terrestrial plants. Significant concentrations of mid-chain n-alkanes (n-C-21-C-25) were detected preferentially in the dark lignites, suggesting that aquatic plants might also have contributed to the plant community during the formation of the dark layers. The content of diterpenoids, and the average ratio of diterpenoids to the sum of diterpenoids and triterpenoids (Di-/(Di- + Tri-terpenoids)) are higher in the pale lignites than in the dark lignites. This indicates that gymnosperms made a crucial contribution to the plant community during the formation of the pale lignites. In the dark lignites, triterpenoids are generally far more abundant than diterpenoids, which suggests that the dark layers were overwhelmingly formed by angiosperm plants. This is consistent with lower C/N ratios in the dark lignite layers (ay. 40.8) compared with the pale lignite layers (ay. 60.6). Higher microbial activities in the pale lignites than in the dark lignites are reflected by the higher concentration of hopanoids and 17 alpha,21 beta-homohopane (22R) in the pale lignites.