Relatively few farmers today actively maintain crop biodiversity, but for most of the history of agriculture this was the norm. Archaeobotanical analyses can reveal the processes that led to the evolution of crop biodiversity throughout the Holocene, an issue of critical importance in an era of climate change and agrobiodiversity loss. Indigenous eastern North Americans domesticated several annual seed crops, called the Eastern Agricultural Complex, beginning c. 1800 BC. Using population morphometrics, this paper reports new evidence for the evolution of a domesticated sub-species of one of these crops, erect knotweed (Polyongum erectum L.), and its subsequent diversification under cultivation. Morphometric analyses were conducted on archaeological erect knotweed populations spanning its ancient cultivated range, and these were directly dated to c. 1–1350 AD, anchoring the evolution of this crop in both time and space. Domesticated erect knotweed first appears c. 1 AD in the Middle Ohio Valley. A diachronic series of populations from western Illinois shows that this species was domesticated again c. 150–1000 AD. This study shows how agricultural knowledge and material were maintained and shared (or not) by communities during an important era in eastern North America’s history: when small communities were aggregating to form the earliest urban center at Cahokia, in the American Bottom floodplain. A distinctive landrace was developed by farmers in the American Bottom which is significantly different from cultivated populations in other regions. Subsequent Mississippian assemblages (c. 1000–1350 AD) indicate divergent agricultural communities of practice, and possibly the eventual feralization of erect knotweed. Archaeobotanical studies have a vast untapped potential to reveal interaction between communities, or their isolation, and to investigate the evolution of crops after initial domestication.