Swertia consists of 150 species with a cosmopolitan geographic distribution and the center of species diversity in the Sino-Himalayan region. Swertia species, especially S. chirayita, have been used extensively in the Nepalese herbal medicine. The author sampled multiple individuals to find whether there are species-specific nucleotide changes to differentiate Swertia species in Nepal. The results indicate that each of the commonly used species has unique sequences and the ITS fragment can be used as a barcoding marker for Swertia in the local medicinal market. Recent phylogenetic studies indicate that Swertia is highly paraphyletic; S. dichotoma and S. tetraptera are more closely related to Halenia than to any other species of Swertia, which do not form a clade. The taxon sampling has been expanded from Nepal to further test the monophyly of Swertia as well as the naturalness of traditionally defined sections. The data support the paraphyly of Swertia relative to other genera of Swertiinae, and highlight the need for reconsidering sections within Swertia. The results from internal transcribed spacer region of the nuclear ribosomal DNA are generally congruent with those of the chloroplast trnL-F sequences. However, there is one well-supported discrepancy between the two genomes. In the ITS tree, Swertia ciliata is positioned in the clade containing S. chirayita and S. lurida, while in the trnL-F tree, it is in the clade of S. dilatata, S. paniculata, S. pedicellata, and S. racemosa. This suggests that Swertia ciliata may have evolved from a hybridization event with S. dilatata, S. paniculata, S. pedicellata, or S. racemosa as the possible maternal parent. Both ITS and trnL-F data support the close relationship of Swertia lurida with S. chirayita. Keywords: Ethnobotany, molecular diffentation, phylogeny, Swertia, taxonomy.