The development of agriculture is one of humankind’s most pivotal achievements. Questions about plant domestication and the origins of agriculture have engaged scholars for well over a century, with implications for understanding its legacy on global subsistence strategies, plant distribution, population health and the global methane budget. Rice is one of the most important crops to be domesticated globally, with both Asia (Oryza sativa L.) and Africa (Oryza glaberrima Steud.) discussed as primary centres of domestication. However, until now the pre-Columbian domestication of rice in the Americas has not been documented. Here we document the domestication of Oryza sp. wild rice by the mid-Holocene residents of the Monte Castelo shell mound starting at approximately 4,000 cal. yr BP, evidenced by increasingly larger rice husk phytoliths. Our data provide evidence for the domestication of wild rice in a region of the Amazon that was also probably the cradle of domestication of other major crops such as cassava (Manihot esculenta), peanut (Arachis hypogaea) and chilli pepper (Capsicum sp.). These results underline the role of wetlands as prime habitats for plant domestication worldwide.