Indigenous cinnamon (Cinnamomum osmophloeum KANEH.) (Lauraceae) is a unique specie of camphor tree in Taiwan. The leaves of cinnamon are rich in essential oils which can be applied to medicine, food and cosmetics. The genetic diversity of seventeen accessions collected in Taiwan were evaluated by RAPD and ISSR markers.The results indicated that both methods revealed high degree of polymorphism and reproduction. A totally 103 amplified DNA fragments were generated by 9 selected RAPD primers and among them 80 fragments show polymorphic. The sizes of DNA fragments were between 3625bp and 250bp. A total 124 amplified DNA fragments, including 105 polymorphic fragments, were generated by 11 selected ISSR primers. The sizes of DNA fragments were between 2500 bp and 250 bp. The ratios of polymorphic DNA fragments produced by RAPD and ISSR were 77.67% and 84.68%, respectively. The similarity between accessions were estimated by using the Dice’s formula based on the total amplified and polymorphic DNA fragments from RAPD and ISSR. The genetic similarity was analysis by UPGMA (Unweighted Pair-Group mean Arithmetic). The results showed that UPGMA cluster analysis based on RAPD similarity matrixs could separate those varieties to seven distinct groups, genetic diversity were between 0.72 and 0.88. The ISSR similarity matrixs could separate those varieties to five distinct groups, genetic diversity were between 0.66 and 0.85
