A recent archaeological survey demonstrates that one of the most durable of all forms of pre-Columbian landscape transformation, Amazonian Dark Earths (ADE; soils formed by pre-Columbian settlement), are widespread along the course of the Madeira River, Central Amazonia, Brazil. We hypothesize that processes of crop cultivation and management by human populations today in landscapes that were intensively transformed during the pre-Columbian period will diverge from those in environments where human agency has not left such a heavy footprint. In order to test this hypothesis, we compare bitter manioc fields, homegardens and secondary forests on ADE with those on non-anthropogenic soils along the lower and middle Madeira River. We demonstrate that crop species and landrace populations diverge on anthropogenic and non-anthropogenic soils as a result of the interaction between human selection and management, soil physical and chemical properties, and plant responses over time. Hence, crop species selection and abundance and therefore agrobiodiversity is contingent on anthropogenic soils in Central Amazonia.