Sour cherry (Prunus cerasus L.) is an agriculturally valuable tree that produces fruits used in a range of culinary dishes, beverages, and other products. The progenitor species and number of origins of sour cherry remain unresolved. Here, we performed phylogenetic analyses of plastid genomes and nuclear genes from nine wild species and three historically important sour cherry cultivars. Our analyses identified Prunus fruticosa and Prunus avium as the closest extant relatives of the progenitor species of tetraploid sour cherry. Furthermore, our analyses revealed P. fruticosa as the likely maternal contributor. These findings and transcriptomic datasets should serve as valuable new resources to guide future breeding efforts in sour cherry.