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Objective: Schisandra sphenanthera and S.chinensis are the two important medicinal plants that have long been used under the names of “Nan-Wuweizi” and “Wuweizi”,respectively.The misuse of “NanWuweizi” and “Wuweizi” in herbal medical products calls for an accurate method to distinguish these herbs.Chloroplast (cp) genomes have been widely used in species delimitation and phylogeny due to their uniparental inheritance and lower substitution rates than that of the nuclear genomes.To develop more efficient DNA markers for distinguishing S.sphenanthera,S.chinensis,and the related species,we sequenced the cp genome ofS.sphenanthera and compared it to that of S.chinensis.Methods: The cp genome of S.sphenanthera was sequenced at the lllumina HiSeq platform,and the reference-guided mapping of contigs was obtained with a de novo assembly procedure.Then,comparative analyses of the cp genomes of S.sphenanthera and S.chinensis were carried out.Results: The cp genome of S.sphenanthera was 146 853 bp in length and consisted of a large single copy (LSC) region of 95 627 bp,a small single copy (SSC) region of 18 292 bp,and a pair of inverted repeats (IR) of 16 467 bp.GC content was 39.6％.A total of 126 functional genes were predicted,of which 113 genes were unique,including 79 protein-coding genes,30 transfer RNA (tRNA) genes,and four ribosomal RNA (rRNA) genes.Five tRNA,four protein-coding genes,and all rRNA were duplicated in the IR regions.There were 18 intron-containing genes,including six tRNA genes and 12 protein-coding genes.In addition,45 SSRs were detected.The whole cp genome of S.sphenanthera was 123 bp longer than that of S.chinensis.A total of 474 SNPs and 97 InDels were identified.Five genetic regions with high levels of variation (Pi ＞ 0.015),trnS-trnG,ccsA-ndhD,psbI-trnS,trnT-psbD and ndhF-rpl32 were revealed.Conclusion: We reported the cp genome ofS.sphenanthera and revealed the SNPs and InDels between the cp genomes of S.sphenanthera and S.chinensis.This study shed light on the species identification and further phylogenetic study within the genus of Schisandra.