| Summary: | Asone of the original plants of traditional Tibetan folk medicinal ‘Zangyinchen’, Swertia franchetiana (S. franchetiana) was used to treat a variety of ailments. Large amount of fruiting harvesting has led to a sharp decrease and gradual depletion of its resources. As a result, the wild resource is on the verge of extinction, it needs urgent conservation. Here, we report the complete sequence of the chloroplast genome of S. franchetiana. The genome was 153,087 bp in length with 130 genes comprising 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of G. paludosa chloroplast genome was is 38.17%. Phylogenomic analysis suggested that S. franchetiana formed a clade with Swertia mussotii with high bootstrap values, indicating that the S. franchetiana was closely related to S. mussotii
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