Abstract: Sequence variation and gene composition of chloroplast genome could effectively reflect the phylogenetic and evolutionary relationships among plants.In this study,DNA libraries were prepared and sequenced by the Illumina Hi Seq,chloroplast genomes of five species of Parnassia and allied genera were assembled respectively,and the structural characteristics,sequence genetic variation and codon preference of protein coding genes of Parnassia chloroplast genome with related species were compared and analyzed.The results showed that the chloroplast genome of Parnassia was conserved tetrad structure,and pseudogenization of several genes were found in P.palustris,but the chloroplast gene composition of other species was the same,encoding 115 genes.Compared with the relative species,the intron of rpl16 gene were lost in all species of Parnassia.The ratio of nonsynonymous/synonymous substitution rate of protein coding genes was low,and chloroplast genes might experience purification selection.Codon preference was consistent with the phylogenetic relationship shown by protein coding sequences.This study reveals that selection pressure may play an important role in the evolution of protein-coding genes in the chloroplast genome of Parnassia,which could enhance the understanding about evolution and adaptation of this genus.