The mantle sources of mid-ocean ridge basalts beneath the Indian and Pacific oceans have distinct isotopic compositions with a long-accepted boundary at the Australian–Antarctic Discordance along the Southeast Indian Ridge. This boundary has been widely used to place constraints on large-scale patterns of mantle flow and composition in the Earth’s upper mantle. Sampling between the Indian and Pacific ridges, however, has been lacking, especially along the remote 2,000 km expanse of the Australian–Antarctic Ridge. Here we present Sr, Nd, Hf and Pb isotope data from this region that show the Australian–Antarctic Ridge has isotopic compositions distinct from both the Pacific and Indian mantle domains. These data define a separate Zealandia–Antarctic domain that appears to have formed in response to the deep mantle upwelling and ensuing volcanism that led to the break-up of Gondwana 90 million years ago, and currently persists at the margins of the Antarctic continent. The relatively shallow depths of the Australian–Antarctic Ridge may be the result of this deep mantle upwelling. Large offset transforms to the east may be the boundary with the Pacific domain.