Gardenia species have been used worldwide for ornamentation and for traditional medicines. The Thailand species observed include eight native species, G. carinata, G. collinsae, G. elata, G. jasminoides, G. obtusifolia, G. saxatilis, G. sootepensis and G. thailandica, and three introduced species, G. gjellerupii, G. taitensis, and G. volkensii. The dendrogram constructed from RAPD banding patterns shows a monophyletic group for each species. Genetic similarity (S) values range from 0.916 to 0.997 for intraspecific level and from 0.651 to 0.816 for interspecific level. The S values are in accordance with similar phenotypic characteristics and a common ancestry of the species, genera, and major groups of chemicals contained within them, such as terpenoids and flavonoids. The standard regions in the genus that could be efficiently used as barcode markers are the trnH-psbA spacer (and combinations of itself), the rbcL, and the matK genes. Genetic distance (D) values of trnH-psbA spacer sequences are 0.005 to 0.481 in intraspecific level, and 0.014 to 0.572 for the interspecific level. The combined sequences give the intraspecific and interspecific D values of 0.004 to 0.102 and 0.008 to 0.178