Subduction followed by underthrusting of continental lithosphere, driven by Oligocene–Early Miocene spreading in the South China Sea marginal basin, account for the tectonic features of Sabah. Isostatic rebound then caused Late Miocene uplift of the Western Cordillera. The strata were buried under 4–8 km of overburden then rapidly exhumed and cooled at >10°C Ma−1. A rate of exhumation of 0.5–0.7 mm a−1 is deduced from thermochronology. The same order of uplift in the Labuk Highlands has exposed metamorphic rocks of the epidote-glaucophane facies. Rapid erosion of the Western Cordillera supplied abundant clastic sediments to the Miocene–Pliocene Baram Delta oil-bearing basin and to the Eastern Lowlands and Sulu Sea.

The Eastern Lowlands were affected by Miocene rifting of the Sulu Sea marginal basin. In contrast to the Western Cordillera, the strata contain apatite crystals whose fission track ages pre-date the containing rocks, indicating burial by only about 2–3 km of overburden. The terrain has been isostatically stable. Some apatite and all zircon crystals, extracted from Tertiary strata, yield Cretaceous fission track provenance ages.

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