Plants of Daphne kiusiana on Jeju Island exhibit morphologically and genetically unique traits. Its taxonomic entity is still unclear and populations are decreasing in size because of human activity. Taxonomic delimitation and conservation efforts are required at the genomic level. We determined the complete chloroplast (cp) genome of this endangered species on Jeju Island, South Korea. Its sequence is 171,491 bp long, and comprises a pair of 41,891 bp inverted repeats, a large-single-copy (LSC) region (85,028 bp), and a diminished small-single-copy region (2681 bp). The cp genome has 135 genes, including 89 that encode proteins, plus 38 tRNAs, and eight rRNAs. Five genes (rpl32, ndhF, accD, clpP, and ndhK) are pseudogenized or lost in its cpDNA. When compared with that of a related species, Aquilaria sinensis, its LSC region contains a large inversion event between rbcL and rps12 that caused pseudogenization of clpP and accD.