Objective   Chloroplast genome structure and phylogeny of the endangered Impatiens omeiana Hook.f. endemic species in China were studied.

  Method  Gene assembly, annotation, characteristics, sequence duplication, and phylogenetics of I. omeiana were analyzed based on the chloroplast genome sequence using bioinformatic software.

  Results   The genome was 152527 bp consisting of 130 gene, including 86 protein-coding, 8 rRNA, and 36 tRNA genes. It had a GC content of 37% and a conservative tetrad structure with regions of a large single-copy of 83150 bp, a small single-copy of 17903 bp, and two identical reverse repeats of 25 737 bp. Thirteen of the genes had one intron, and two had two. There were 76 SSR sequences detected in the genome mainly of A/T single nucleotides with a length ranging from 10 bp to 91 bp. A total of 50842 codons were found in the entire genome. Among the amino acids, leucine (Leu) was the most numerous and tryptophan (Tyr) the least. A codon bias analysis showed those of 33 RSCU＞1 had A/U on their ends. Using the Neighbor Joining method (NJ), a phylogenetic tree was constructed based on the chloroplast genomes from different plants to show a close relationship of I. omeiana with I. guizhouensis belonging to the subgenus Clavicarpa.

  Conclusion  The chloroplast genome of I. omeiana had a typical tetrad structure of many SSR repeated sequences with A/T single base. Phylogenetically, I. omeiana was a Clavicarpa subgenus. These results provide important molecular information for the phylogenetic status and species identification of I. omeiana.