Oil palm (Elaeis guineensis) is one of the most important oil-bearing crop in the world. This crop can be vegetatively propagated only using tissue culture technique. Oil palm tissue culture technique has low efficiency, with callogenesis and embryogenesis stages as the limiting factors. Genetic factor has a major role in determining the success rate of these two stages. The use of molecular markers which represent the rate of embryogenesis or callogenesis has the potential to improve the efficiency of oil palm tissue culture process. In this study, SNP mining was conducted on embryogenesis transcriptome data, oil palm cDNA database, oil palm genome database, and oil palm SNPs marker database in NCBI. The objective of this study was to obtain SNP marker which represents the embryogenesis potential, to be further used in marker assisted selection of oil palm ortets. One SNP (EMB6) showed significant association with embryogenesis rate. This SNP was found in one of Auxin Response Factor (ARF) family gene. Nucleotide replacement from Adenine to Guanine changed the 307th amino acid from Isoleucine to Methionine. Oil palms with Adenine homozygote (A/A) pattern on the EMB6 showed 8-fold higher chance to produce significantly higher embryogenesis rate than Adenine-Guanine heterozygote (A/G).