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Aiming to examine whether the genetic background of the crude drugs derived from four Yunnanese <i>Swertia</i> plants and their chemical constituent profiles correlate, we analyzed the nucleotide sequences of their nuclear ribosomal DNA regions including ITS1, 5.8S ribosomal RNA gene, and ITS2, together with those of Japanese <i>S. japonica</i> and <i>S. pseudochinensis</i> from Hebei Province. The result that two of the Yunnanese <i>Swertia</i> plants, <i>S. binchuanensis</i> and <i>S. punicea</i>, were genetically similar may explain their similarity in chemical constituent profiles. On the other hand, in spite of differences in chemical profile, <i>S. decora</i> and <i>S. pseudochinensis</i> were genetically close. The other Yunnanese <i>Swertia</i> plants, <i>S. delavayi,</i> and <i>S. japonica</i>, stood at intermediate positions between these two genetically similar pairs. The result suggests that although genetic background would have an influence, environmental factors, e.g., soil and weather conditions, might be critical for their production of secondary metabolites.