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Palaeozoic era (540–250 Ma)

During the Cambrian period, Gondwana had a mild climate. West Antarctica was partially in the Northern Hemisphere, and during the time, large amounts of sandstones, limestones, and shales were deposited. East Antarctica was at the equator, where seafloor invertebrates and trilobites flourished in the tropical seas. By the start of the Devonian period (416 Ma), Gondwana was in more southern latitudes, and the climate was cooler, though fossils of land plants are known from then. Sand and silts were laid down in what is now the Ellsworth, Horlick and Pensacola Mountains.

Antarctica became glaciated during the Late Paleozoic icehouse beginning at the end of the Devonian period (360 Ma), though glaciation would substantially increase during the late Carboniferous. It drifted closer to the South Pole, and the climate cooled, though flora remained. After deglaciation during the latter half of the Early Permian, the land became dominated by glossopterids (an extinct group of seed plants with no close living relatives), most prominently Glossopteris, a tree interpreted as growing in waterlogged soils, which formed extensive coal deposits. Other plants found in Antarctica during the Permian include Cordaitales, sphenopsids, ferns, and lycophytes. At the end of the Permian, the climate became drier and hotter over much of Gondwana, and the glossopterid forest ecosystems collapsed, as part of the End-Permian mass extinction. There is no evidence of any tetrapods having lived in Antarctica during the Paleozoic.