Abstract: 【Objective】This research sequenced the complete chloroplast genome of Impatiens macrovexilla and I.macrovexilla var. yaoshanensis,so as to compare and analyze their differences in genome structure,and to construct the phylogenetic relationships of 20 Impatiens species. The phylogenetic results would provide basis for further confirming earlier botanical classifications of these two taxa,as well as benefiting the application and genetic improvement of germplasm resources.【Method】The genomic DNA of I. macrovexilla and I. macrovexilla var. yaoshanensis were sequenced by using the BGISEQ-500 platform. The Fastp software and the NOVOPlasty v.2.6.2 program were used to assemble the final chloroplast genome. The chloroplast genomes were annotated with the CpGAVAS online tool;the other bioinformatics software including MAFFT v.7.0,CAIcal,REPuter,MISA,and FastTree were used for sequence alignment,relative synonymous codon usage(RSCU)for the protein-coding genes,location of the repeat sequences,the simple sequence repeats(SSRs)and a maximum likelihood(ML)phylogenetic trees.【Result】The established circular genome of I. macrovexilla and I. macrovexilla var. yaoshanensis had 36.77% and 36.80% of GC contents,which contained 152437 and 152286 bp,respectively. These two genomes included a large single-copy(LSC)region of 83331 and 83212 bp,a small single-copy(SSC)region of 17376 and 17312 bp,and a pair of inverted repeats(IRa and IRb)of 25865 and 25881 bp,respectively.Both of two genomes presented with 88 protein-coding genes,8 rRNA genes,37 tRNA genes and no pseudogenes. The phylogenetic dendrogram analysis revealed that,species classification within the genus Impatiens were consistent with the earlier botanical classification based on systematic morphological analysis. Even though the chloroplast of I. macrovexilla and I. macrovexilla var. yaoshanensis were genetically very close,they formed two distinct species rather than the subspecies level proposed by former botanists.【Conclusion】I. macrovexilla and I. macrovexilla var. yaoshanensis would be separated as two individual species. Some genetic variation in chloroplast,especially the identified SSR loci can be used for species identification and population genetics studies.