Palm oil is a versatile vegetable oil that is a major contributor to the world’s edible oil market. The importance of the crop led to the use of biotechnology to better understand and further improve its performance. Initial efforts were focused on the identification of genes and markers associated with specific traits. Although these efforts provided some insights, they were unable to identify the causal genes and mutations relevant to the traits. The major advance came with the introduction of next-generation sequencing, which provided a cost-effective way to sequence the oil palm genome. The publication of the genome sequence in 2013 resulted in the identification of the SHELL, Virescens (VIR) and MANTLED genes. The genome sequence also accelerated the identification of genomic regions influencing other complex traits, such as height and fatty acid composition, and facilitated comparative genomics analyses. This review describes the developments of oil palm biotechnology research, and diagnostic assays for SHELL, VIR and MANTLED traits. The assays have practical applications in improving the efficiency of oil palm breeding and tissue culture. The genomics and epigenomics-based approaches have started to provide the necessary tools that will support the sustainable development of oil palm.