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Current evidence suggests that Southeast Asia was occupied by Hoabinhian hunter-gatherers until ~4000 years ago, but the human occupation history thereafter with farming economies remains unsettled. By sequencing 26 ancient human genomes (25 Southeast Asians, 1 Japanese Jomon), the history is shown to be more complex than previously thought; both Hoabinhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity. The results help resolve one of the long-standing controversies in Southeast Asian prehistory.