The assessment of genetic diversity and genetic structure of natural oil palm populations is carried out mostly for crop improvement purpose. A set of 16 microsatellite markers was used to genotype 494 palms from 49 populations belonging to ten African countries, three breeding and one semi-wild materials. The number of alleles per locus varied from 8 to 22, making a total of 209 alleles over the 16 microsatellite markers. The effective number varied from 1.1 in all populations from Madagascar to 4.7 in population 40 from Nigeria (mean = 3.30. Mean expected heterozygosity was high (0.644) ranging from 0.033 in population 3 from Madagascar to 0.803 in population 40 from Nigeria. The average genetic distance among oil palm populations was 0.684. An UPGMA cluster analysis showed three main clusters. One cluster grouped accessions from Madagascar while populations from Senegal, Guinea and Sierra Leone formed the second cluster. Populations from Ghana, Nigeria, Cameroon, Zaire, Angola, Tanzania and the breeding materials formed the third cluster. The grouping of Deli MPOB and Deli Dabou breeding materials into the same sub-cluster confirmed their common origin. The results acquired lead to redefining new strategies to make the most of the new genetic resources in oil palm improvement.