The genus Hill belongs to the tribe Potentilleae Sweet and contains approximately 75 species predominantly distributed in the Sino-Himalayan region and the Malesian archipelago. So far we have less knowledge on the phylogenetic relationships within owing to limited sampling of taxa or gene fragments in previous studies. Moreover, to date there is no phylogenetic study on from the perspective of comparative chloroplast (cp) genomics. Here we performed comparative genomic analyses on the cp genomes of 39 accessions representing 18 taxa of . The cp genomes presented the typical quadripartite structure, with the sizes ranging from 155 096 bp to 157 166 bp. The 39 cp genomes contained a set of 112 unique genes, comprising four ribosomal RNA (rRNA) genes, 30 transfer RNA (tRNA) genes, as well as 78 protein-coding genes (PCGs). The cp genome organization, gene content and order in were highly conserved, but some visible divergences were present in IR/SC boundary regions. Ten regions () were identified as excellent candidate DNA markers for future studies on species identification, population genetics and phylogeny of . Our results indicated that is monophyletic. In the current sampling, the - clade was sister to the remainder of . Our results corroborated the previous taxonomic treatments to transfer and from the genus L. to . Our results showed close relationships among , , , and , congruent with previous studies based on the morphology of these species. Twenty-six genes () were with sites under positive selection, and adaptive evolution of these genes might have played crucial roles in species adaptation to the harsh mountain environment. This study will facilitate future work on taxonomy, phylogenetics, and adaptive evolution of .