Organic geochemistry of Gondwana coals, especially the distribution of molecular fossils or biomarkers, is not well constrained, throughout the world. In this study, we have, therefore, evaluated biomarker signatures along with bulk organic matter and petrographic characteristics in coal samples collected from two Gondwana Basins in India – Satpura Basin (Kanhan coalfield) and Damodar Valley Basin (Jharia coalfield). From both coalfields, the samples were collected from the Lower Permian Barakar Formation, which is one of the major coal bearing strata in India. A significant variation in thermal maturity levels in the samples is indicated by Rock-Eval pyrolysis and petrographic analysis–with the Kanhan samples generally belonging to immature to early-mature stage, while the Jharia samples display characteristics of overmature coals. This variation in the thermal maturity strongly affects the biomarker distributions. Especially, the terpenoids, hopanes and steranes were considerably degraded due to thermal maturation and were below detection limit in the overmature samples. Presence of aliphatic diterpanes, ent-16α(H)-kaurane, 16α(H)-phyllocladane as well as aromatic diterpanes, retene, methylretenes, tetrahydroretene, simonellite and bisnorsimonellite in low maturity samples indicate terrestrial input, possibly, from the primitive conifers. However, the aliphatic and aromatic diterpanes were below detection limit in overmature samples making it difficult to infer their source. Distributions of polycyclic aromatic hydrocarbons (PAHs) are also controlled by thermal maturity levels, as evident from difference in PAH ratios in the low and high maturity samples.