Molecular biodegradation indices for extracts from five Pennsylvanian coals and six New Albany Shale (Devonian - Mississippian) samples from the eastern part of the Illinois Basin help constrain relationships between the degradation of biomarkers and the generation of coalbed methane and shale gas. Investigation of these gas source rocks of varying thermal maturity from different depths facilitates evaluation of the association of microbial degradation with biogenic gas formation distinct from thermogenic processes. Extensive biodegradation of both aliphatic and aromatic hydrocarbons is observed in the coal extracts, whereas in shale extracts only short-chain (C-15-C-19) n-alkanes from the shallowest depth appear to be microbially altered with minimal evidence for losses of acyclic isoprenoid alkanes and aromatic hydrocarbons. By contrast, biodegradation of aromatic hydrocarbons, specifically alkylated naphthalenes and phenanthrenes, occurs in coal extracts in concert with losses of n-alkanes attributable to microbial activity. Thus, the progress of hydrocarbon biodegradation in coals differs from the sequence recognized in petroleum where the effects of microbial alteration of aromatic constituents only appear after extensive losses of aliphatic compounds. The extent of hydrocarbon biodegradation in these coals also decreases with depth, as recorded by the Sigma(nC(25)-nC(30)) index (i.e. abundance relative to 17 alpha(H), 21 alpha(H)-hopane) among the aliphatic constituents and several aromatic compounds (methyl-, dimethyl-, and trimethylnaphthalenes, phenanthrene, and trimethyl- and tetramethylphananthrenes). However, the depth variations in the distributions of aliphatic and aromatic hydrocarbons in the shale extracts primarily reflect the effects of thermal maturity rather than biodegradation. Overall, variations in the extent and patterns of biomarker biodegradation among coals and shales likely reflect their distinct microbial consortia that can be attributed to differences in (i) surviving microorganisms and inoculations from meteoric water, (ii) the characteristics of the sedimentary organic matter, especially the preponderance of aromatic constituents in coals, and (iii) the accessibility to that substrate through pores and cleats. These results help constrain the processes involved in biodegradation and controls on its extent, which, in turn, assist in recognizing sites favorable for methanogenesis and improved estimates of biogenic gas resources in the Illinois Basin. (C) 2012 Elsevier B.V. All rights reserved.