The lower middle Mississippian limestones (Fort Payne, Burlington-Keokuk, Ullin, and Warsaw Formations) in the Illinois Basin resemble the modern cool-water Heterozoan Association, consisting mainly of crinoidal-bryozoan remains. This is in contrast to the upper middle Mississippian limestones (e.g., Salem, St. Louis, Ste. Genevieve Limestone), which are typically oolitic and peloidal with common peritidal facies, similar to the warm-water Photozoan Association. A Heterozoan-like limestone facies belt also characterizes the Lower Devonian carbonate successions in the Illinois Basin. The prevalence of Heterozoan carbonates during the early part of the middle Mississippian correlates with a rapid increase in the rate of subsidence and a major second-order eustatic sea-level rise that resulted in relatively deep-water basins at this time. In the Illinois Basin, this event is represented by deposition of a relatively thick siliceous, spiculitic, and radiolarian-bearing limestone (e.g., Fort Payne Formation and deep water facies of the Burlington-Keokuk Limestone). A similar depositional pattern occurred in the basin during the Early Devonian period, when several hundred meters of siliceous and cherty carbonates were deposited in deeper water settings that were flanked by coarse, crinoidal grainstone facies on the basin margin. Upwelling of cool, nutrient- and silica-rich deep oceanic water that entered the Illinois Basin were probably responsible for the proliferation of pelmatozoans and bryozoans during the Early Devonian and early middle Mississippian time. The subsequent change from cool-water-like carbonate to warm-water-like carbonate deposition appears to be related to decrease in subsidence and gradual shallowing of the basin. Porosity and permeability of the middle Mississippian and Lower Devonian carbonates appear to be primarily controlled by the relative abundance of crinoidal fragments, which are susceptible to rapid cementation by syntaxial calcite. As a result, the best hydrocarbon reservoirs are generally developed within the bryozoan-dominated carbonates, which were especially prevalent during the early part of the middle Mississippian.