Potentilla freyniana Bornm. has radical leaves with petioles and trifoliolate distinguished from Potentilla fragarioides and Duchesnea indica. In this study, we presented first complete chloroplast genome of P. freyniana to understand its phylogenetic position. Its length is 156,381 bp long and has four subregions: 85,724 bp of large single copy (LSC) and 18,617 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 phylogenetic position of P. freyniana disagrees with three phylogenetic studies, showing that more Potentilla chloroplast genomes are required for clarifying Potentilla phylogeny.