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The beginning of plant cultivation is one of the most important cultural transitions in human history 1 – 4 . Based on molecular markers showing the genetic similarities between domesticated plants and wild relatives, south-western Amazonia has been proposed as one of the early centres of plant domestication 4 – 6 . However, the nature of the early human occupation and the history of plant cultivation in south-western Amazonia are still little understood. Here, we document the cultivation of Cucurbita at ca. 10,250 cal yr BP, Manihot at ca. 10,350 cal yr BP and Zea mays at ca. 6,850 cal yr BP in the Llanos de Moxos. We show that, starting ca. 10,850 cal yr BP, pre-Columbians created an anthropic landscape made of approximately 4,700 artificial forest islands within a treeless seasonally flooded savannah. Our results confirm the Llanos de Moxos as a hotspot for early plant cultivation and demonstrate that ever since their arrival, humans have caused a profound alteration of Amazonian landscapes, with lasting repercussions for habitat heterogeneity and species conservation.

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We report on previously unknown early archaeological sites in the Bolivian lowlands, demonstrating for the first time early and middle Holocene human presence in western Amazonia. Multidisciplinary research in forest islands situated in seasonally-inundated savannahs has revealed stratified shell middens produced by human foragers as early as 10,000 years ago, making them the oldest archaeological sites in the region. The absence of stone resources and partial burial by recent alluvial sediments has meant that these kinds of deposits have, until now, remained unidentified. We conducted core sampling, archaeological excavations and an interdisciplinary study of the stratigraphy and recovered materials from three shell midden mounds. Based on multiple lines of evidence, including radiocarbon dating, sedimentary proxies (elements, steroids and black carbon), micromorphology and faunal analysis, we demonstrate the anthropogenic origin and antiquity of these sites. In a tropical and geomorphologically active landscape often considered challenging both for early human occupation and for the preservation of hunter-gatherer sites, the newly discovered shell middens provide evidence for early to middle Holocene occupation and illustrate the potential for identifying and interpreting early open-air archaeological sites in western Amazonia. The existence of early hunter-gatherer sites in the Bolivian lowlands sheds new light on the region’s past and offers a new context within which the late Holocene “Earthmovers” of the Llanos de Moxos could have emerged.