AbstractPrunus mongolicais an ecologically and economically important xerophytic tree native to Northwest China. Here, we report a high-quality, chromosome-levelP. mongolicagenome assembly integrating PacBio high-fidelity sequencing and Hi-C technology. The assembled genome was 233.17 Mb in size, with 98.89% assigned to eight pseudochromosomes. The genome had contig and scaffold N50s of 24.33 Mb and 26.54 Mb, respectively, a BUSCO completeness score of 98.76%, and CEGMA indicated that 98.47% of the assembled genome was reliably annotated. The genome contained a total of 88.54 Mb (37.97%) of repetitive sequences and 23,798 protein-coding genes. We found thatP. mongolicaexperienced two whole-genome duplications, with the most recent event occurring ~3.57 million years ago. Phylogenetic and chromosome syntenic analyses revealed thatP. mongolicawas closely related toP. persicaandP. dulcis. Furthermore, we identified a number of candidate genes involved in drought tolerance and fatty acid biosynthesis. These candidate genes are likely to prove useful in studies of drought tolerance and fatty acid biosynthesis inP. mongolica, and will provide important genetic resources for molecular breeding and improvement experiments inPrunusspecies. This high-quality reference genome will also accelerate the study of the adaptation of xerophytic plants to drought.