Abstract: Taking Allium mongolicum as test material, the chloroplast genome was sequenced by Illumina NovaSep high-throughput sequencing technology, and the chloroplast genome microsatellites were searched and analyzed by using MISA v1.0 software, in order to provide reference for the species identification, population genetics and phylogenetic studies of A.mongolicum.The results showed that a total of 260 SSR sites were detected on the 153 376 bp chloroplast genome sequence of A.mongolicum.One SSR locus occurred per 590 bp on average, mainly distributed in the large copy region.There were 5 repeat types, of which the largest number of single nucleotide repeat type accounted for 66.79%,followed by trinucleotide（23.99%） and the least number of pentanucleotide, accounting for only 0.37%.The cpSSR was 8-29 bp, mainly in the range of 8-10 bp（75.77%）,of which 9 cpSSR were 20 bp and above in length, indicating that the cpSSR on the chloroplast genome of A.mongolicum have a high polymorphic potential.