Abstract: In order to understand the chloroplast genome structure and variation of medicinal plants in Chloranthus, the chloroplast genomes of five medicinal plants in Chloranthus were obtained on NCBI, and the characteristics, repeat sequences, IR region contraction and expansion and variation sites of chloroplast genomes were studied by bioinformatics methods, and the phylogenetic tree was reconstructed. The chloroplast genomes of the five species have similar gene content, gene order and GC content, ranging from 157 063 to 158 758 bp, and the total number of genes is 132-136. Mononucleotide, dinucleotide, trinucleotide, tetranucleotide and compound repeat sequences were detected in five plants of Chloranthus.Pentanucleotide was only detected in C. angustifolius, C. henryi and C. serratus, and hexanucleotide was only detected in C. angustifolius. The boundary expansion and contraction genes of the five species are quite different. The coding regions of matK, psbK, atpI, petN, rps4, ycf4, petD and other genes, and the non-coding regions of trnQ-UUG, trnS-GCU, trnC-GCA, trnT-GGU, trnL-UAA and other intergenic regions vary greatly.The phylogenetic analysis showed that the genetic relationship between C. fortunei and C. serratus was close, and the genetic relationship between C. angustifolius and the other four species was far. The results will provide an important basis for the subsequent molecular marker development, phylogeny and genome evolution analysis of medicinal plants in Chloranthus.