The global ridge system is dominated by oceanic rises reflecting large variations in axial depth associated with mantle hotspots. The little-studied Marion Rise is as large as the Icelandic Rise, considering both length and depth, but has an axial rift (rather than a high) nearly its entire length. Uniquely along the Southwest Indian Ridge systematic sampling allows direct examination of crustal architecture over its full length. Here we show that, unlike the Icelandic Rise, peridotites are extensively exposed high on the rise, revealing that the crust is generally thin, and often missing, over a rifted rise. Therefore the Marion Rise must be largely an isostatic response to ancient melting events that created low-density depleted mantle beneath the Southwest Indian Ridge rather than thickened crust or a large thermal anomaly. The origin of this depleted mantle is probably the mantle emplaced into the African asthenosphere during the Karoo and Madagascar flood basalt events.