The complete plastid genome of Gentiana leucomelaena Maxim., belonging to the most species-rich section Chondrophyllae in Gentiana , was determined and analyzed in this study. It has a circular-mapping molecular with the length of 131,856 bp, the shortest one among all available Gentiana plastomes. Gentiana leucomelaena has gene mutation, for example ndh and rpl 2 intron, and reversed SSC region comparing with the available species in sections Cruciata , Frigida , Kudoa , Isomeria and Microsperma . Phylogenetic analysis showed that G. leucomelaena clustered together with section Cruciata with a long branch. The plastome provides in this work will contribute to elucidate the phylogenetics and evolution in Gentiana .