Scientific research has suggested that maize spread from Mexico and arrived in lowland South America in a state of partial domestication. However, archaeological samples with primitive morphological characteristics that corroborate this finding have not been recorded in the region thus far. Unexpectedly, many samples were identified in the Peruaçu Valley with characteristics never previously observed in South America. These archaeological samples with primitive characteristics, which are the focus of this work, represent the furthest records from the center of origin of the species and the longest duration of the maintenance of such characteristics (between 1010 and 570 years before present). The findings of this study, including archaeological samples, native races, and samples of teosinte, attest to a long history of maize diversification in lowland South America.