DNA based molecular markers have a potential utility in herbal medicine analysis and widely used for studying genetic relationship of medicinal plant species. Therefore, this study aims to assess the genetic relationship among eleven Gardenia species collected from different locations in Thailand using random amplified polymorphic DNA (RAPD) marker. Ninety primers were initially screened, out of which 20 primers generated 579 reproducible bands of different sizes with an average of 28.95 bands per primer. The mean percentage of polymorphic bands was 99.5%. Similarity index ranged from 0.089 to 0.332. The highest similarity index (0.332) was found between Gardenia lineata and G. jasminoides while the lowest similarity index (0.089) was found between G. carinata and G. sootepensis. A dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA) and can be divided into 2 distinct clusters which correlated with their morphological characteristics.
