Sustainable development of a breeding programme depends on having sufficient genetic variability to achieve genetic gains in each selection cycle. The aim of this study was to molecularly characterize families of the oil palm, Elaeis guineensis Jacq., of different origins using microsatellite molecular markers. The value of the observed heterozygosity was higher than that of the expected heterozygosity in all of the progenies. The coefficients ( G ST = 0.207 and F ST = 0.174) and AMOVA showed genotypic differences among the evaluated families. Likewise, this was reflected in the groups obtained by the dendrogram and principal coordinate analyses. This difference could have evolved due to the enrichment of some of the families with germplasm from different origins. Therefore, genetic relationships estimated from molecular data would be convenient to select families more distant from each group and palms more distant from each family selected to reserve genetic variability. This information will guide us in the decision-making process when planning breeding programmes focused on crosses to develop new populations with an acceptable broad genetic base and adaptability. In this way, sources of resistance to biotic and abiotic factors can be identified for the development of new varieties with competitive advantages for the sector.