Rosa willmottiae Hemsl. (1907) is an ornamental plant with certain medicinal value. Its complete chloroplast genome was assembled via high-throughput sequencing. The 157,277 bp circular genome comprises one large single-copy region (LSC; 86,207 bp), one small single-copy region (SSC; 19,264 bp) and two inverted repeat regions (IRs; 25,903 bp each), encoding 130 genes: 86 protein-coding genes, 36 tRNAs and 8 rRNAs. Phylogenetic analyses indicate Rosa willmottiae’s closest affinity to Kushui Rose (R. sertata × R. rugosa), and strongly support Rosa willmottiae’s role as the putative maternal progenitor of Kushui Rose. This study contributes to the understanding of evolutionary relationships within the genus Rosa.
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