Chloroplast genome sequences have comprehensive application prospects in DNA barcoding and chloroplast engineering in traditional Chinese medicine.  The complete chloroplast genome of Magnolia officinalis sequenced by high-throughput pyrosequencing and a sequencing procedure was established.  Fourteen contigs were obtained after de nove assembly.  The sequencing percent of coverage was 99.99%.  The chloroplast genome is 160 183 bp in size, and has a typical quadripartite structure with the large (LSC, 88 210 bp) and small copy (SSC, 18 843 bp) regions separated by two copies of an inverted repeat (IRs, 26 565 bp each).  126 chloroplast genes were successfully annotated, of which 17 genes located in each IR region.  The chloroplast genome features in Magnolia officinalis are nearly identical to those from other Magnoliid chloroplast genomes.  Phylogenetic analyses were performed based on 81 shared coding-genes for a total of 9 Magnolia samples of 5 closely related species.  Results showed that distinguishing among species was generally straightforward at the species and population level.  This study confirmed the effectiveness of our chloroplast genome sequencing procedure.  The chloroplast genome can provide distinguishing differences to help identify Magnolia officinalis and its closely related plants.