AbstractSour cherry (Prunus cerasusL.) is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors closely related to extantPrunus fruticosa(ground cherry) andPrunus avium(sweet cherry). Here we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency, the predominant cultivar grown in the USA. We also generated a draft assembly ofP. fruticosato use alongside a publishedP. aviumsequence for syntelog-based subgenome assignments for ‘Montmorency’ and provide compelling evidenceP. fruticosais also an allotetraploid. Using hierarchal k-mer clustering and phylogenomics, we show ‘Montmorency’ is trigenomic, containing two distinct subgenomes inherited from aP. fruticosa-like ancestor (A and A') and two copies of the same subgenome inherited from aP. avium-like ancestor (BB). The genome composition of ‘Montmorency’ is AA'BB and little-to-no recombination has occurred between progenitor subgenomes (A/A' and B). InPrunus, two known classes of genes are important to breeding strategies: the self-incompatibility loci (S-alleles), which determine compatible crosses, successful fertilization, and fruit set, and theDormancy Associated MADS-boxgenes (DAMs), which strongly affect dormancy transitions and flowering time. TheS-alleles andDAMsin ‘Montmorency’ andP. fruticosawere manually annotated and support subgenome assignments. Lastly, the hybridization event ‘Montmorency’ is descended from was estimated to have occurred less than 1.61 million years ago, making sour cherry a relatively recent allotetraploid. The ‘Montmorency’ genome highlights the evolutionary complexity of the genusPrunusand will inform future breeding strategies for sour cherry, comparative genomics in the Rosaceae, and questions regarding neopolyploidy.