As part of our ongoing phylogenetic study of genus Hypericum, nuclear ribosomal DNA internal transcribed spacer sequences were analyzed for 36 species of Hypericum as ingroup and two species of Thornea as outgroup. This sampling included most of the previously described species from both Korea and Japan. The ITS phylogeny suggested that the surveyed Hypericum species belong to a monophyletic section, Trigynobrathys, and a polyphyletic section, Hypericum. In addition, two monotypic sections, Sampsonia and Roscyna, were identified. Members of section Hypericum occur in four different lineages worldwide, which imply at least four independent origins. The Korean and Japanese species of section Hypericum form a monophyletic group, except for H. vulcanicum. Instead, that particular species belongs to a distinct monophyletic group with H. scoreri and H. formosa from other geographic areas, and is a sister to section Trigynobrathys. The Korean and Japanese species of section Trigynobrathys show a monophyletic origin. H. sampsonii is now recognized as a distinct section rather than being a member of sections Hypericum or Drosocarpium, as had been indicated previously. Our results differ somewhat from those of recent morphological and cytological studies. The phylogenetic relationships among Korean and Japanese species have now been mostly resolved via ITS phylogeny.