The extent of genetic diversity among 494 oil palms from 49 populations (representing ten African countries, three breeding materials, and one semi-wild material) were assessed using 16 SSR markers. The genetic diversity was high with a total of 209 alleles detected accounting for an average of 13.1 alleles per locus and a mean expected heterozygosity of 0.644. The average genetic distance among accessions was 0.769, varying from 0.000 to 1.000. Both principal coordinates analysis and neighbor joining tree, confirmed by structure analysis, clustered the entire collections into three groups: the Extreme West Africa (EWA) group (collections from Senegal, Guinea, and Sierra Leone), the West, Central, and East Africa (WCEA) group (collections from Ghana, Nigeria, Cameroon, Zaire, Angola, Tanzania, Bahia, the semi-wild material and the two Deli breeding materials) and the Madagascar group (collections uniquely from Madagascar). Madagascar populations were found to be genetically distinct from all other African populations. The influence of human and environmental factors might have played a major role in grouping the African natural oil palm into three different groups as well as in the formation of a transition zone (formed by Ghana and Côte d'Ivoire). Further analysis of genetic structure revealed Deli materials as a distinct population within the WCEA group. Given the fact that accessions were exchanged between the EWA and WCEA groups, intra- and inter-group combinations for breeding should be based mainly on the genetic distance between accessions to increase yield and heterosis.