It has long been disputed whether Prunus yedoensis was originated from Mt. Halla in Cheju-do or Cheju-do originated taxon is the same as the cultivated one from Japan. By comparing the base sequences in the ITS 1, ITS 2 and 5.8s coding region of the nuclear ribosomal DNA, genetic relationship was assessed between P. yedoensis Matsumura-Native and P. yedoensis Matsumura-Cultivar. There showed three sites of point mutation (base substitution) and seven insertions or deletions in 236bp of ITS 1 but no differences in 164 bp of 5.8s coding region. On the other hand, it was shown that four sites of point mutation (base substitution) and seven insertions or deletions in 233 bp of ITS 2. The content of (G+C) in ITS 1 region was 59.4% in natives and 60.2% in cultivar and in ITS2, 64.0% in natives and 64.3% in cultivar, respectively. But the 5.8s coding region was identical as 56.3% in each taxon. The ida that P. yedoensis Matsumura-Native would be different from the P. yedoensis Matsumura-Cultivar would be strongly substantiated from the similar results obtained in this studies with those of previous studies.