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Investigations in the now-submerged cave systems on the Yucatán Peninsula continue to yield evidence for human presence during the Pleistocene-Holocene transition. Skeletal remains are scattered throughout the caves of Quintana Roo, most representing individuals who died in situ. The reasons why they explored these underground environments have remained unclear. Here, we announce the discovery of the first subterranean ochre mine of Paleoindian age found in the Americas, offering compelling evidence for mining in three cave systems on the eastern Yucatán over a ~2000-year period between ~12 and 10 ka. The cave passages exhibit preserved evidence for ochre extraction pits, speleothem digging tools, shattered and piled flowstone debris, cairn navigational markers, and hearths yielding charcoal from highly resinous wood species. The sophistication and extent of the activities demonstrate a readiness to venture into the dark zones of the caves to prospect and collect what was evidently a highly valued mineral resource.