Abstract: Taking the chloroplast genome of Allium tuberosum as the research object,the chloroplast genome was sequenced by Illumina NovaSep sequencing platform and the structure,codon preference,simple repeat sequence,comparison and phylogeny of chloroplast genome were studied,in order to provide reference for the molecular marker development,identification and exploitation of the germplasm resources studies of A.tuberosum.The results showed that the chloroplast genome of A,tuberosum was 154 056 bp in length with 133 genes annotated,including 38 tRNAs,8 rRNAs and87 protein-coding genes.The codons in cpDNA of A.tuberosum tended to end with A or U,the frequency of Leu was the highest and that of Cys was the lowest.250 SSR loci were identified in the chloroplast genome sequence,with the highest number of single nucleotide repeats（164） and the lowest number of hexanucleotide repeats（one）.There were no obvious expansion and contraction at the IR boundaries;phylogenetic analysis showed that A.tuberosum was most closely related to A.ramosum.