In Amazonia there are at least 85 arboreal species with domesticated populations, among which piquiá [Caryocar villosum (Aubl.) Pers.] is widely distributed. In some regions, there is ethnobotanical evidence of domestication for its fruit. To understand more about piquiá domestication, we evaluated genetic diversity and structure of two regions, sampling 130 trees in forests and homegardens (92 trees in the Tapajós National Forest and 38 in the Rio Ouro Preto Extractive Reserve), using seven microsatellite markers. In Tapajós, piquiá trees form large aggregations near archaeological sites, while in Ouro Preto the aggregations are smaller. The Tapajós presented higher effective number of alleles, allelic richness and expected heterozygosity, with lower observed heterozygosity and, consequently, a higher fixation index and lower apparent outcrossing rate. Genetic structure exists between regions, forming four probable groups: one that corresponds mainly to Ouro Preto and the others in the Tapajós. When the Tapajós was analyzed separately, we found four genetic groups that do not correspond to homegarden and forest systems. In the homegardens we found lower number of effective alleles, allelic richness and observed heterozygosity. These subtle differences in genetic diversity between homegarden and forest trees identify piquiá’s incipient domestication, agreeing with ethnobotanical evidence. The piquiá stands near archaeological sites and the existence of four genetic groups suggest that piquiá was introduced into the Tapajós during pre-Columbian times from at least three different sources. Trail registration numbers: SisBio—58609-1, from August 5, 2017; SisGen—A3D06AA, from March 26, 2020.
