Late Atokan-early Desmoinesian permineralized peats of the Kalo Formation from the Williamson #3 Mine in south-central Iowa contain the oldest known gymnosperm-dominated community from a paleotropical swamp. While other Iowa deposits of similar age are dominated by a mixture of cordaitalean gymnosperms, tree ferns, and medullosan gymnosperms, fifty-three percent of the Williamson #3 peat accumulated in communities dominated by cordaitalean gymnosperms and forty-two percent accumulated in communities dominated by medullosan gymnosperms. Near synchronous changes in Pennsylvanian swamp vegetation indicate two major paleoclimatic changes. Early gymnosperm-dominated peats, like the Williamson #3 peat, probably formed in a climate in which vegetation was exposed to seasonally dry conditions. In the mid-to-late Desmoinesian, climate became wetter and lycopsids replaced gymnosperms as the dominant vegetation in swamps. In the Missourian, the climate once again became relatively dry, and tree ferns and seed ferns replaced lycopsids in the swamps. The seed fern and tree fern swamp associations of the Atokan-early Desmoinesian and Missourian are similar at the generic level. Early seed fern and tree fern communities that persisted in refugia during the interval of wet climate in the mid-to-late Desmoinesian could have expanded into Missourian swamps as climates became seasonally drier. Thus, paleoclimatic variation plays an important role in determining the dominant vegetation in these Pennsylvanian swamps with stressed genera existing in localized areas where climatic conditions favorable for their growth persist.