Potentilla stolonifera var. quelpaertensis Nakai has developed stolon in comparison to Potentilla fragarioides var. major. To uncover phylogenetic relations of two species, we presented complete chloroplast genome of P. stolonifera var. quelpaertensis which is 156,393 bp long and has four subregions: 85,763 bp of large single-copy (LSC) and 18,590 bp of small single-copy (SSC) regions are separated by 26,020 bp of inverted repeat (IR) regions including 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 36.9\% and those in the LSC, SSC, and IR regions are 34.8\%, 30.7\%, and 42.7\%, respectively. Phylogenetic trees show that P. stolonifera var. quelpaertensis is closely clustered with P. fragarioides var. major and Potentilla centigrana, of which morphological characteristics are clearly distinct with each other. Additional researches are strongly required to understand the relationship between morphological classification and phylogenetic relationship of these Potentilla species.