Efforts by the Malaysian Palm Oil Board (MPOB) to sequence the hypomethylated regions of several individual palms using the GeneThresherTM methylation filtering technology enabled the discovery of over 20,000 SNPs in the gene-rich regions of the oil palm genome. Based on several criteria, a set of 1,536 oil palm SNPs was chosen for Illumina Golden Gate® assay design. By genotyping an F2-selfed mapping population that segregates for the fruit colour trait with this SNP set, 297 SNP markers were selected and positioned on the genetic map constructed using this mapping population. Several SNP markers linked to the fruit colour gene have been identified. This trait is important as the palms can be distinguished based on the colour of their fruit coats. The two most common types are nigrescens and virescens. The virescens palms are preferred as the fruits undergo a more profound color change on ripening, thus making it easier for harvesters to identify ripened bunches. The linkage of these SNP markers to the virescens trait was also tested on several independent crosses of different genetic backgrounds using the Golden Gate® Genotyping Assay with Veracode Technology®. Our results have indicated the ability of these markers to predict fruit colour with an accuracy of greater than 90% in the crosses tested. This will facilitate the identification of virescens palms through a marker-assisted selection approach.