Cultivated flowering cherries (Prunus subgenus Cerasus), which are one of the most popular ornamental trees around the world, have been developed through artificial hybridizations among wild flowering cherries. Among the hundreds of cultivars of flowering cherries, Prunus ×yedoensis ‘Somei-yoshino’ is the most common and widespread. However, its origin and genetic relationship to wild P. yedoensis, naturally occurring on Jeju Island, South Korea, have long been debated. We used sequence polymorphisms in eight chloroplast DNA (cpDNA) noncoding regions to distinguish wild and cultivated flowering cherries among 104 individuals (55 accessions). We were able to distinguish two distinct groups, one corresponding to wild P. yedoensis collections from Jeju Island and the other collections of cultivated P. ×yedoensis from Korea, Japan, and the United States. The chlorotype diversity of wild P. yedoensis in Jeju Island and cultivated P. ×yedoensis collections in the United States was quite high, suggesting multiple natural hybrid origins and long history of cultivation from different original sources, respectively.