The characteristic of complete chloroplast (cp) genome of Magnolia sieboldii, an endangered species in China, was first sequenced in this study. It showed a typical quadripartite structure with a length of 160,177bp. It composed of a large single copy (LSC) region of 88,238bp, a small single copy (SSC) region of 18,763bp, and a pair of inverted repeat (IR) regions of 26,588bp. Further maximum parsimony phylogenetic analysis was performed based on 38 complete plastomes from 30 magnoliids and basal angiosperm species. The result supported a close relationship among M. grandiflora, M. officinals, M. sieboldii, and M. tripetala.