Ammopiptanthus nanus, one of the tertiary relict plants, is a rare evergreen broad-leaved shrub in desert region of mid-Asia. The plant species can grow in environment with extremely high level of drought and freezing stress, and it can be used as a model for stress tolerance research in tress. However, research in A. nanus at molecular level is hindered by the lack of genome information. In the present study, flow cytometry analysis was performed to predict the genome size of A. nanus. Genomic survey sequencing of A. nanus was then conducted, and a total of 65 Gb sequencing reads was obtained. K-mer analysis using these sequencing reads was conducted to predict the genome size, heterozygosity and GC content of A. nanus. The genome size of A. nanus was estimated to be 770-787 Mb. The total reads length of contigs is 0.538 Gb, with a N50 of 684 bp, and after further assembly, the N50 of scaffords is 12.09 Kb with a total reads length of 0.602 Gb. SSR molecular markers were predicted using the assembled genome sequences and 151858 SSR were obtained. Of all SSR categories, the dinucleotide repeat units is largest, with a percentage of 56.39%, and the AT/TA components is the dominant dinucleotide repeat unit. Our study reported on the genomic characteristics of A nanus for the first time, and provided a large number of genomic sequences for further research in A nanus.