Using museum and literature data, we characterize faunal turnover in bivalves and brachiopods of the North American Midcontinent over approximately 12.5 Myr spanning the Pennsylvanian/Permian boundary. The two groups experienced indistinguishable rates of background faunal turnover but differed in the type and timing of elevated turnover episodes. Bivalves underwent an episode of elevated first appearance in the Missourian Series whereas brachiopods underwent an episode of elevated disappearance in the Wolfcampian Series. In neither group does turnover history strongly correlate to long-term changes in basinal lithofacies, which reflect evolution of regional climate. Comparison with other time intervals and basins suggests that magnitude and frequency of turnover episodes during the late Paleozoic was intermediate between the more episodic early Paleozoic and less episodic Mesozoic.