The morphology, mineralogy, and stratigraphic and lateral distribution of paleosols in Pennsylvanian (Moscovian–Gzhelian; Atokan–Virgilian) mixed marine and terrestrial coal-bearing strata (i.e., cyclothems) in the Illinois basin (IB) are presented in order to determine the dominant pedogenic processes within a cyclic sedimentary depositional framework. Paleosol morphologies range from weakly developed horizons with evidence of rooting and little to no pedogenic structure, to horizons with well-developed pedogenic slickensides, angular blocky structure, and carbonate nodules and tubules. The majority of paleosols in strata from the basin interior preserve (1) low chroma (gley) colors, (2) identifiable fossil plant organic matter that increases in abundance upward in the profiles toward the interpreted paleo-surface, and (3) calcite, sphaerosiderite, and pyrite cements and nodules. In contrast, paleosols in strata from the northern margin of the basin display high chroma colors and calcite cements and less fossil organic matter, sphaerosiderite, and pyrite cements. These observations indicate that paleosols from the basin interior underwent a multi-phase pedogenic and shallow burial history characterized by an initial better-drained, oxygenated stage under seasonal precipitation, followed by a poorly drained, reducing stage, while paleosols from the northern margin of the basin experienced overall more oxygenated conditions throughout their pedogenic development. X-ray diffraction analysis of the < 2 µm size fraction of paleosol matrix in IB paleosols indicates a mineralogical composition dominated by kaolinite, randomly interstratified (R0) and ordered (R1) illite–smectite (I/S), and subordinate amounts of chlorite. These combined observational and mineralogical datasets indicate that significant changes in paleohydrology were largely responsible for the development of Pennsylvanian soil profiles in the IB.