Abstract Background Astrocaryum aculeatum is a palm tree species native to the tropical regions of South America, exploited commercially by local farmers for the pulp extracted from its fruits. The objective of this research was to compare the genetic diversity between adult plants and seedlings from open-pollinated seeds, quantify the pollen flow and dispersal, the spatial genetic structure, and the effective size of a population that has been continuously harvested for its fruits. The study was carried out in a natural population of A. aculeatum distributed over approximately 8 ha in the State of Amazonas (Brazil), separated by 400 m from the closest neighboring population. In total, 112 potential pollen donors, 12 mother plants and 120 offspring were mapped and genotyped. Results Genetic diversity was high for parents and the offspring. The fixation indexes for adults (F = -0.035) and offspring (F = -0.060) were negative and not significant. A significant spatial genetic structure was detected for the adult plants (up to the distance of 45 m) indicating short-distance seed dispersal. Paternity analysis detected 9.2 % of pollen immigration and the average distance of pollination within the population was 81 m. The average effective pollination neighborhood area between plants was 1.51 ha. Conclusions Our results indicate that substantial introduction of new alleles has occurred in the population through pollen immigration, contributing to the maintenance of genetic diversity. Conservation efforts aimed at maintaining the gene pool of the current population or establishing new populations should utilize offspring from mother plants selected to be spaced by at least 50 m to prevent collecting seeds from relatives. ; The authors thank the Fundação de Amparo à Pesquisa do Estado do Amazonas (FAPEAM) for a scholarship to SLFR and supporting the project "Publicação de Artigos Científicos em Genética e Melhoramento de Plantas" - PAPAC (process 062.02685 / 2014); the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for scholarships to AMS, MTGL, EAV; the Embrapa Amazônia Ocidental through the project “Pesquisa, desenvolvimento e inovação em palmáceas para a produção de óleo e aproveitamento econômico de coprodutos e resíduos – PROPALMA” (process 01.10.0343.00); and the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) - Programa de Excelência Acadêmica (Proex) of the Genetics Department of ESALQ-USP for supporting this research; and the Laboratório Temático de Biologia Molecular - Instituto Nacional de Pesquisas da Amazônia (LTBM – INPA) for its facilities. The authors also thank Mrs. Angela Mary Wray for the great contribution in the English language and two anonymous reviewers for the excellent suggestions in the manuscript.