Abstract:In order to understand the characters of chloroplast genome (cp genome) in Paris polyphylla var. chinensis, the chloroplast genome (cp genome) of P. polyphylla var. chinensis was compared with those of 10 species within Liliales by using phylogenomics methods based on complete chloroplast genomes. The results showed that the cp genome of P. polyphylla var. chinensis was 158307 bp in length and display a typical quadripartite structure including two inverted repeat regions (IRA and IRB, 27473 bp), one small singlecopy region (SSC, 18175 bp) and one large single-copy region (LSC, 85187 bp). It contained 115 unique genes, including 81 protein-coding genes, 30 tRNAs and 4 rRNAs. The genome structure, gene contents and arrangement of 10 Liliales species cp genomes were very similar. The cemA gene of P. polyphylla var. chinensis was pseudogene with poly(A) and CA SSR patterns after the start codon, and the loci of premature stop codons are different from those of Paris veticillata. In conclusion, the cp genome of P. polyphylla var. chinensis was conservative. The cemA structure and pseudogenization might play an important role in the evolution and phylogeny, and the location of the stop codons in cemA was useful for distinguishing P. polyphylla var. chinensis from P. veticillata.