Permian coals from Blackwater, Poitrel and Moura (Bowen Basin, Queensland) have been extracted and characterised by detailed organic geochemical techniques. A variety of source-related aliphatic and aromatic biomarker parameters indicate that these coals from three different locations are similar in terms of organic matter type and palaeoenvironment of deposition. The hydrocarbons extracted from these coals appear to have been generated from predominantly plant-derived organic matter deposited in a fluvio-deltaic environment. Moderately high Pr/Ph ratios, the high proportion of C29 steranes and very low sterane to hopane ratios are indicative of their largely terrestrial source. Molecular maturity parameters derived from aliphatic and aromatic biomarkers corroborate a measured maturity of 1.0–1.1% Ro for these medium volatile bituminous coals.The aliphatic and aromatic hydrocarbon distributions in these coals also allow their differentiation into two groups: biodegraded Moura coals and non-degraded Blackwater and Poitrel coals. Comparison of various compound ratios from the degraded and non-degraded coals indicate the dependence of susceptibility to biodegradation on precise molecular structures. Major aromatic compound classes in coals, generally regarded as being more resistant, may be microbially altered before branched/cyclic alkanes are affected and even before the n-alkanes are completely removed. As reported in crude oils, susceptibility to biodegradation of aromatic hydrocarbons decreases with increasing number of aromatic rings and with increasing number of alkyl substituents. Furthermore, alkylnaphthalenes with 1,6-dimethyl substitution patterns are more susceptible to degradation than other alkylnaphthalene isomers. This study reveals that biodegradation may alter the hydrocarbon composition of coals in a similar way to that observed in crude oils or oil spills, except that aromatic hydrocarbons are altered relatively earlier than aliphatic hydrocarbons in coals compared to oils.