is a flowering cherry germplasm resource for ornamental purposes. In this work, we present a de novo chromosome-scale genome assembly of by the use of Nanopore and Hi-C sequencing technologies. The assembled genome is 265.40 Mb across 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb. It contains 29,094 coding genes, 27,611 (94.90%) of which are annotated in at least one functional database. Synteny analysis indicated that and have 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 of are distributed on all chromosomes of , implying that chromosome 01 is the most ancient or active of the chromosomes. The comparative genomic analysis confirmed that has 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families. By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The present species diverged from ~17.34 million years ago (Mya), while the divergence of and was estimated to have occurred ∼21.44 Mya. In addition, a total of 148 MADS-box family gene members were identified in , accompanying the loss of the AGL32 subfamily and the expansion of the SVP subfamily. The MYB and WRKY gene families comprising 372 and 66 genes could be divided into seven and eight subfamilies in , respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searching within the PRGdb. This research provides high-quality genomic information about as well as insights into the evolutionary history of species.