In this study, a set of seven simple sequence repeat (SSR) markers were developed for Japanese maple, and the genetic diversity of 107 Japanese maple cultivars was estimated using these markers. A total of 87 alleles were detected, ranging from 4 to 25 per locus, with an average of 12.43 alleles per locus. Most cultivars showed unique SSR profiles, indicating that the markers were effective for cultivar identification, while some pairs of bud-sport cultivars and synonyms showed identical SSR

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... files. Principal component analysis (PCA) indicated that 107 Japanese maple cultivars were divided into two groups: one consists of cultivars of Acer palmatum, and the other group includes cultivars of two varieties, A. amoenum var. amoenum and A. amoenum var. matsumurae. Analysis of molecular variance (AMOVA) revealed significant differentiation between the two species, while the genetic differentiation and distance between the two varieties of A. amoenum were very low, with F ST = 0.026 and D = 0.057, respectively. Thus, the two varieties of A. amoenum are genetically indistinguishable from each other in domesticated cultivars, while most cultivars of A. palmatum have been developed separately from those of A. amoenum.