Distinct assemblages of paleosols above and below the Permian–Triassic boundary in the Karoo Basin of South Africa are evidence for reorganization of ecosystems following this greatest of all mass extinctions. The Permian–Triassic boundary is recognized from the last appearance of Dicynodon and from a series of negative excursions in the isotopic composition of carbon within therapsid tusks, pedogenic carbonate nodules, and organic matter. The boundary is also marked by laminated beds with very weakly developed paleosols, a change from purple (10R) to brownish red (2.5YR) paleosols, and a thin (10-cm) claystone breccia of reworked soil clasts. Paleoclimatic changes include a shift from arid and highly seasonal paleoclimate inferred from diffuse and shallow calcareous nodules in Permian paleosols to semiarid and less seasonal paleoclimate inferred from deep and well-focused calcic horizons in Triassic paleosols. An earliest Triassic shift to warmer and wetter paleoclimate is also indicated by increased chemical weathering, abundance of lycopsids, and diversity of labyrinthodonts. Permian paleosols have root traces comparable to those of open shrubland and riparian woodland, whereas Triassic paleosols have root traces and profile forms like soils of open woodland. This is a significant paleoenvironmental change, but not as dramatic a change as would be expected from the devastating extinctions of 88% of fossil vertebrate genera. Latest Permian therapsid reptiles were diverse and ecologically specialized. In contrast, the principal earliest Triassic therapsid, Lystrosaurus, was a burrower with no specific habitat preference. Its short internal nares, barrel chest, and high neural spines would have given it greater aerobic scope than preexisting therapsids and may have been an advantage under conditions of hypercapnia and hypoxia. These adaptations and associated ecosystem changes are compatible with widespread vertebrate mortality by acidosis and pulmonary edema in a post-apocalyptic greenhouse created by the voluminous release of methane from shallow marine and permafrost clathrates.