Mauritia flexuosa dominated palm swamps are an important forest resource covering over 30,000 km2 across the Amazon basin. In Ecuadorean Amazonia, Mauritia flexuosa, a dioecious and arborescent palm species, forms small and isolated populations or large and dense stands on poorly drained soils. How these populations are genetically interconnected and how genetic diversity varies between cohorts of different ages remains little studied although they are important for conservation of these ecosystems. The genetic structure of Mauritia flexuosa was studied in five natural stands using eight microsatellite loci and two cohorts (seedling and adults). In addition, age structure and sex ratio within the stands were assessed using transects. The age structure of the studied Mauritia flexuosa stands is represented by a high number of seedlings (mean = 1,153.6/ha) and adults (mean = 563.2/ha), with a sex ratio favoring female individuals (1.42:1). These stands are also characterized by a fine‐scale genetic structure, high observed heterozygosity (mean: HO seedlings=0.52; HO adults=0.52), high inbreeding (mean: FIS seedlings = 0.26; FIS adults = 0.26), low number of migrants (Nm=0.29), strong genetic differentiation (mean: pairwise RST/ D‐values seedlings = 0.08/ 0.74; mean RST/D‐values adults = 0.17/ 0.76), and an average effective population size (Ne) of 191.42 individuals. No intergenerational genetic variation was detected between seedlings and adults. We suggest that the high genetic diversity and inbreeding as well as the strong differentiation among stands of these populations could be explained, at least partially, by a low genetic connectivity among populations. Destructive harvesting of its fruits and defaunation will be major threats to Mauritia flexuosa populations in the future. Abstract in Spanish is available with online material

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