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The diversity of juçara palm (Euterpe edulis) must be investigated at the molecular level to enable the adoption of appropriate management strategies that may associate breeding studies with conservation. With the aim of describing the genetic diversity and structure of a population of E. edulis in a commercial plantation area, the genotyping of 199 individuals was performed using nine nuclear microsatellite markers. We detected inbreeding in the population and the diversity within the plots was high showing diversity among the individuals. The individuals from matrices germplasm of the locality Santa Marta, were divergent. The diversity indices observed in the studied population were close to those reported in the literature for natural populations; thus, the ex situ conservation of the population in this managed is feasible, as is their potential use in breeding studies.