Both the inferred thermal regime and the variation in crustal thickness beneath the Southern Alps suggest that the mode of crustal shortening changes substantially along the length of the Alpine fault. North of Mt. Cook, crustal shortening is being accommodated predominantly by uplift and erosion of Pacific plate continental crust, as postulated in the Wellman-Adams tectonic model. However, south of Mt. Cook, the absence of high heat flow and a large crustal root that is not in isostatic equilibrium may have resulted from underthrusting of as much as 100 km of Indian plate continental crust.