Understanding of genetic diversity and its distribution is essential for promoting the use of genetic resources. The development of core collections using molecular tools has been proposed as a strategy for increasing the economical use and conservation of genetic resources. In this study, we investigated the genetic variation among different geographical origins and potential entries that constituted a core collection of oil palm, using 29 microsatellite markers and by evaluating 788 oil palm accessions. Our results revealed important genetic diversity (H T= 0.759) between oil palm accessions from Angola and Cameroon, which exhibited a low coefficient of genetic differentiation between populations (G ST= 0.022). However, the inclusion of oil palm accessions from Indonesia in the analysis resulted in a high coefficient of genetic differentiation between populations (G ST= 0.251). We found that the combination of stratified sampling based on a sorting method and a heuristic algorithm was the most effective method for the development of an oil palm core collection set. Using this method, two core collections were identified. The first core collection, comprising 289 entries, contained 271 retained alleles in a sample representing 37% of the entire collection. The second one is a mini core collection, comprising 91 entries, that contained 271 retained alleles with a total H e value of 0.72 in a sample representing 11% of the entire collection. The information reported in this study will be of great interest to oil palm researchers because new strategies for breeding programmes can be developed based on these advances.