Genetic variation among flowering cherries (Prunus subgenus Cerasus) was characterized by SSR markers developed from peach, sweet cherry and sour cherry, using a total of 144 individuals from 15 taxa. Twenty-five out of 85 SSR markers showed amplification in all tested samples, indicating that 29% of SSRs developed from related species could be transferred to flowering cherries. In contrast, 25 SSRs gave no amplification for any tested samples. The mean number of alleles per locus and the mean number of n_e (the effective number of alleles per locus) assessed by 9 transferable SSRs were 17.3 and 7.3, respectively. All but 2 individuals were distinguished by 9 SSR loci. Genetic variation among flowering cherries was higher than that in peach and sweet cherry cultivars. On the other hand, the mean number of alleles per locus on each taxon ranged from 1.9 to 7.7, suggesting that each taxon accounted for a rather small part of the variation of flowering cherries. A phenogram of 144 individuals and a phenogram of 14 taxa based on SSR analysis were constructed. Many taxa were clustered in the sections to which they belong. Four taxa of section Incisae were closely related. Two taxa of section Apetalae were also closely related. P. maximowiczii and P. pendula f. ascendens were distant from the other Japanese taxa. These results were in good accordance with the morphological classification. We found the SSR markers developed from related species useful for evaluating the genetic variation and clustering flowering cherries.