Oceanic hotspots with extreme enriched mantle radiogenic isotopic signatures—including high 87Sr/86Sr and low 143Nd/144Nd indicative of ancient subduction of continental crust—are restricted to the southern hemispheric mantle. However, the mechanisms responsible for concentrating subducted continental crust in the austral mantle are unknown. We show subduction of sediments and subduction eroded material, and lower continental crust delamination, cannot generate this spatially coherent austral domain. However, late Neoproterozoic to Paleozoic continental collisions—associated with the assembly of Gondwana and Pangea—were positioned predominantly in the southern hemisphere during the late Neoproterozoic appearance of widespread continental ultra-high-pressure (UHP, >2.7 gigapascals) metamorphic terranes, which marked the onset of deep subduction of upper continental crust. We propose that deep subduction of upper continental crust at ancient rifted-passive margins during austral supercontinent assembly, from 650-300 Ma, resulted in enhanced upper continental crust delivery into the southern hemisphere mantle. In contrast, EM domains are absent in boreal hotspots, for two reasons. First, continental crust subducted after 300—when the continents drifted into the northern hemisphere—has had insufficient time to return to the surface in plumes feeding northern hemisphere hotspots. Second, before the appearance of continental UHP rocks at 650 Ma, upper continental crust was not subducted to great depths, thus precluding its subduction into the northern hemisphere mantle during the Precambrian when continents may have been located in the northern hemisphere. Our model implies a recent formation of the austral EM domain, explains the geochemical dichotomy between austral and boreal hotspots, and may explain why austral hotspots outnumber boreal hotspots.