Oil palm (Elaeis guineensis Jacq.) belongs to the Arecaceae family and is the largest source of edible vegetable oil worldwide. Micropropagation of oil palm by somatic embryogenesis takes a long time from callus initiation to the production of plantlets. This research project aims to investigate the genes involved in somatic embryogenesis of oil palm during the tissue culture process. We applied the cDNA-AFLP technique to identify genes associated with somatic embryogenesis in oil palm during the tissue culture process. Sixty-four EcoRI/MseI AFLP primer combinations produced a total of 1449 transcription-derived fragments (TDF), of which 1193 TDF (82.33%) showed polymorphism. The most abundant up-regulated and down-regulated transcripts during somatic embryogenesis were selected for characterisation. Sixtyfive TDF were sequenced, and 34 distinct sequences were obtained. Primer pairs were successfully designed for 18 of these sequences. The differential expression of the 18 distinct sequences was analysed by using semi-quantitative RT-PCR. The information obtained from this study provides prior knowledge about the genetic underlying the somatic embryogenesis in oil palm, and will be the starting point that reveals the genetic components and mechanism in the control of this process in the future.