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The characteristics of the evolution of the South Asian monsoon during the late Miocene through the Pliocene are highly debated. To obtain a better understanding, we studied the clay mineral assemblages and the clay fraction content of a high-quality sedimentary sequence (borehole core ZK1) spanning the interval of 8.8-2.62 Ma in the Zhaotong Basin, southwestern Yunnan Province, on the southeastern margin of the Tibetan Plateau. Smectite, kaolinite, illite and vermiculite were the four main clay minerals identified, and changes in their relative abundance reveal a distinct pattern of climate change during the study interval. Until the very late Miocene kaolinite and smectite, with a small amount of illite, were dominant, suggesting a relatively warm and humid climate; from -6.2 to -2.8 Ma smectite was dominant, with a minor amount of kaolinite and illite, indicating a relatively cool and humid climate; and from -2.8 to 2.62 Ma vermiculite (HIV) and illite were dominant, with a minor amount of kaolinite, indicating a relatively cold and humid climate. The variation in clay mineral assemblages indicate substantial changes in the South Asian monsoon in the Zhaotong Basin that promoted a change from a warm and humid climate in the late Micoene to cool and humid climate in the very late Miocene through Pliocene, followed by a gradual trend towards a cold and humid climate in the very late Pliocene. Comparison with records from elsewhere indicates that the observed variations in the South Asian monsoon were mainly controlled by global cooling rather than by Tibetan Plateau uplift.