New candidate of variety of Potentilla, named as Potentilla freyniana var. chejuensis, was found in about 1,000–1,500 m elevations in Mt. Halla in Korea. To uncover its phylogenomic relationships with available chloroplast genomes, we presented complete chloroplast genome of P. freyniana var. chejuensis which is 156,739 bp long and has four subregions: 85,909 bp of large single copy (LSC) and 18,590 bp of small single copy (SSC) regions are separated by 25,940 bp of inverted repeat (IR) regions including 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs). The overall GC content of the chloroplast genome is 36.9\% and those in the LSC, SSC, and IR regions are 34.7, 30.7, and 42.8\%, respectively. Phylogenomic trees based on whole chloroplast genomes show that P. freyniana var. chejuensis is clustered with three Potentilla species isolated in Korea which present enough differences of their morphologies. It indicates that P. freyniana var. chejuensis can be a new variety species.