Here, we report a completely sequenced plastome using Illumina/Solexa sequencing-by-synthesis (SBS) technology. The plastome of Magnolia kwangsiensis Figlar & Noot. is 159 667 bp in length with a typical quadripartite structure: 88 030 bp large single-copy (LSC) and 18 669 bp small single-copy (SSC) regions, separated by two 26 484 bp inverted repeat (IR) regions. The overall predicted gene number is 129, among which 17 genes are duplicated in IR regions. The plastome of M. kwangsiensis is identical in its gene order to previously published plastomes of magnoliids. Furthermore, the C-to-U type RNA editing frequency of 114 seed plants is positively correlated with plastome GC content and plastome length, whereas plastome length is not correlated with GC content. A total of 16 potential putative barcoding or low taxonomic level phylogenetic study markers in Magnoliaceae were detected by comparing the coding and noncoding regions of the plastome of M. kwangsiensis with that of Liriodendron tulipifera L. At least eight markers might be applied not only to Magnoliaceae but also to other taxa. The 86 mononucleotide cpSSRs that distributed in single-copy noncoding regions are highly valuable to study population genetics and conservation genetics of this endangered rare species.