The narrow genetic diversity coupled with intensive selection has reduced the variability of yield components and vegetative traits of oil palm breeding populations. Thus, the objective of the current study is to evaluate the genetic variability of oil palm breeding populations using AFLP markers. The eight AFLP primer pairs utilised in this study generated 228 bands across 67 populations. As expected, populations created from intercrossing revealed relatively higher levels of genetic diversity compared with those derived from selfings. The dendrogram and Principal Component Analysis (PCA) of the DxD palms indicated a high genetic similarity. Among palms from the TxT/P crosses, the groupings were aligned according to the agency, signifying the accumulation of distinctive sets of alleles, likely due to the different selection pressure imposed by the respective agency. In PCA, the TxT palms, however, revealed a close genetic relationship indicating the need for incorporating new genetic resources to widen the genetic base. Based on the results, it is recommended the introduction of new genetic resources into the dura and tenera/pisifera populations. Additionally, crossing palms from populations of high genetic distances and adopting intercrossing scheme should result in off-springs with considerable diversity for selection gain in future breeding programmes.