Abstract: Allium chinense belongs to the genus Alliums of the lily family. It can be used both as medicine and food. To date, the phylogenetic relationship of Allium species have not be resolved completely. Furthermore, there has been a lack of DNA barcode to distinguish closely related species. In this study, the complete chloroplast genome of A. chinense was obtained using next generation DNA sequencing and bioinformatic analysis, and compared with that from other Allium species. The genome is a circular molecule of 152 525 bp with a typical quadripartite structure. Genome annotation identified a total of 116 genes, including 81 protein-coding genes, 31 tRNA genes, and 4 rRNA genes. Analyses of sequences from six Allium species showed that the most diverse regions are found in the protein coding regions such as ndhA and ycf1 genes, and in the intergenic regions, such as ps16-trnQ, trnT-trnF, ndhF-rpl32, rpl32-trnL and rpl16-rps3. A phylogenetic tree was constructed using 58 protein coding sequences from 53 species. All branches showed strong support with bootstrap scores reaching 66%-100%, except those for the Lilium and Paris. Our results suggest that the completed chloroplast genome could solve the classification problems of these species. Using EcoPrimer software, we identified seven markers from the chloroplast genomes, which can be used to differentiate congeneric species. In summary, we have sequenced the complete chloroplast genome of A. chinense, carried out phylogenetic analysis and identified a series of genus specific DNA barcode sequences. The results have laid the foundation for the systematical determination of the phylogenetic relationship of Allium species and the differentiation of species using the genus specific primers.