Illumina sequencing platform was used to obtain the whole chloroplast genome sequences of Ardisia crenata. Compared with the structural characteristics and variation degree of chloroplast genomes based on bioinformatics methods, this study is aimed to clarify the characteristics and differences of the chloroplast genomes of A. crenata and Ardisia crenata var. bicolor, to compare and analyze the chloroplast genomes, and to provide reference for the phylogenetic study of Myrsinaceae. As results, both of them were composed of one large single copy region（LSC）, one small single copy region（SSC）and a pair of reverse repeat regions（IRa/IRb）. Total 132 genes were annotated, and their repeat sequence types and distribution patterns were similar, but the number was different. The results of comparative genomics showed that the coding regions of psbA, matK, rpoC2, ropB, ndhK, accD, ndhF, ndhD, ndhH and ycf1 genes were different, and they provided new loci for molecular identification of Ardisia. The chloroplast genome of A. crenata and A. crenata var. bicolor was highly conserved, and there was no rearrangement or inversion between chloroplast genomes. The variation of IR region sequence was the lowest, and the variation degree of SSC region was the highest. In the phylogenetic tree, the A. crenata and A. crenata var. bicolor were sister groups, which clearly reflected the genetic relationship, and provided a scientific explanation for the variety of A. crenata from molecular level. The Myrsinaceae and Primulaceae can be divided into two branches according based on the support rate. In this study, the chloroplast genome structure of A. crenata was analyzed, and the phylogenetic relationship among the genera of Myrsinaceae was discussed, which lays a foundation for the study of taxonomic identification, phylogenetic evolution and resource exploitation and utilization of medicinal plants of Myrsinaceae.
