Cerasus ｘ yedoensis ‘Somei-yoshino’ Fujino, one of the most popular flowering cherry cultivars in Japan, is considered a hybrid of Cerasus spachiana and Cerasus speciosa. In the present study, 27 microsatellite marker loci on the genetic linkage map of ‘Somei-yoshino’ were genotyped in the wild populations of C. spachiana and C. speciosa. Based on the allele frequencies in the wild population, two alleles of ‘Somei-yoshino’ were assigned to each of them. Of the 54 alleles analyzed, 44.4 and 33.3％ were assigned to C. spachiana and C. speciosa, respectively. The remaining 22.2％ were unidentified because of their equal frequencies or rare observations in both species. In addition, some chromosomes consisted of two regions derived from C. spachiana and C. speciosa, respectively. These results suggested that some ‘Somei-yoshino’ chromosomes were formed by the crossing-over of hybrid ancestors. Thus, we concluded that ‘Somei-yoshino’ may not have originated from a simple hybrid such as a first filial generation, but from a more complicated crossing between C. spachiana and C. speciosa.