Tissue culture is a promising technology for mass propagation of high yielding oil palm. However, the large scale production of clonal palm is still not optimal. The application of DNA marker for early diagnosis of high quality ortets (selected oil palm tree for cloning) would greatly help in reducing the production cost. Representational difference analysis (RDA) was used to identify genomic differences between the oil palm explant tissues of the same genotypes but producing different somatic embryogenesis rates in culture. The putative RDA products isolated were cloned, sequenced and verified. Among the products isolated, C1-20 and C14-19 from forward and reverse RDA respectively, possess a single nucleotide change when aligned with the equivalent DNA region of the subtracted tissues. However, further verification is needed to confirm the discriminating effects of these products on the fecundity of the selected ortets.