Melliodendron xylocarpum Handel-Mazzetti is a rare tree, distinct member of the family Styracaceae. In this study, we determined the complete chloroplast (cp) genome sequence of M. xylocarpum in an effort to provide genomic resources useful for promoting its conservation. The entire cp genome was determined to be 157,165 bp in length. It contains the typical structure and gene content of angiosperm plastome, The plastome contains a large single-copy (LSC) and a small single-copy (SSC) regions of 90,193 and 18,486 bp, respectively, which were separated by a pair of 24,243 bp inverted repeat (IR) regions. The genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC content of M. xylocarpum genome is 37.21%. The complete plastome sequence of M. xylocarpum will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Styracaceae. Phylogenetic analysis revealed that M. xylocarpum is closely related to Changiostyrax dolichocarpus H.S.Lo & D.Fang, but forms an independent evolutionary branch.