Owing to their significant medicinal and edible values, the natural
Dendrobium
species have underdone over-collection and habitat destruction, and cultivated species emerged for candidates. However, these
Dendrobium
plants are similar in shape to be easily confused, leading to extreme difficulties for identification based on their morphological and chemical features. In this study, the rDNA ITS region sequence analysis was developed for rapid and accurate identification of thirteen wild and cultivated
Dendrobium
species belonging to two sections
Formosae
and
Chrysotoxae
. By cloning and sequencing the rDNA ITS region genes from 13
Dendrobium
species, the phylogenetic relationships among them were analyzed. Results showed that the variation of the ITS region, together with the lengths and Guanine and Cytosine contents of ITS, 5.8s rDNA, ITS1 and ITS2 sequences occurred in the tested
Dendrobium
species, and which from section
Chrysotoxae
was higher than that from section
Formsae
. Phylogenetic analysis based on neighbor-joining and maximum p-arsimony trees indicated that the
Dendrobium
species of sections
Formosae
and
Chrysotoxae
could be well divided into two groups. A majority of
Dendrobium
species exhibited distinctive ITS2 secondary structures, while for those with close genetic relationships were similar. Therefore, the ITS2 region sequence analysis is simple, quick, and highly reliable that can be used as an effective tool for molecular identification and classification, as well as the reconstruction of the phylogeny of wild and cultivated
Dendrobium
species belonging to different sections.