Abstract: Applying 41977 expressed sequence tags (EST) of oil palm released in NCBI, 3946 SSR loci were identified. We designed primers for 27 SSR loci based on their flanking sequences and conducted amplification in 18 oil palm DNA samples. The amplification result showed that 10 SSR markers were polymorphic. According to the ten SSR makers, we used Principle Component Analysis to elucidate population structure of the 18 oil palm germplasm. Principle Component Analysis demonstrated that the 18 oil palm germplasm could be classified into two genetic groups: one was composed of oil palm germlasm collected from Gaolong bay and coconut institution in Wenchang city; the other including germplasm introduced from Malaysia. This study showed that developed SSR markers could be used for characterization of genetic diversity, population structure and construction of genetic map for oil palm.