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Abstract The Transantarctic Mountains (TAMs), Antarctica, exhibit anomalous uplift and volcanism and have been associated with regions of thermally perturbed upper mantle that may or may not be connected to lower mantle processes. To determine if the anomalous upper mantle beneath the TAMs connects to the lower mantle, we interrogate the mantle transition zone (MTZ) structure under the TAMs and adjacent parts of East Antarctica using 12,500+ detections of P-to-S conversions from the 410 and 660 km discontinuities. Our results show distinct zones of thinner-than-global-average MTZ (∼205–225 km, ∼10%–18% thinner) beneath the central TAMs and southern Victoria Land, revealing throughgoing convective thermal anomalies (i.e., mantle plumes) that connect prominent upper and lower mantle low-velocity regions. This suggests that the thermally perturbed upper mantle beneath the TAMs and Ross Island may have a lower mantle origin, which could influence patterns of volcanism and TAMs uplift.