The genus Quercus comprises approximately 500 species distributed throughout the Northern Hemisphere. There are three major distribution centers in the world including North America, Europe and Eastern Asia. The Eastern Asia show the highest species diversity and almost 250 species are recognized in this region. Many primitive species of Quercus are also recognized in this region. In order to elucidate the phylogeny and distribution patterns of the Asian Quercus species, we reconstructed the phylogeny of the Quercus species based on the three noncoding region sequences of chloroplast genome and ITS sequences of nuclear rDNA. The combined noncoding region phylogeny of chloroplast genome show the good resolution among most species groups. However, the species relationships among very closely related species were unresolved. The phylogeny are more congruent to the geographical distribution patterns of the species than the infrageneric classification system even though the phylogeny largely congruent to the currently recognized subgenus, section, and series. The ITS phylogeny also largely congruent to the chloroplast DNA phylogeny, however, more than two copies of ITS sequences are recognized from a same individual. We cloned and sequenced two or three ITS types from several species. Thus, more cautious data interpretation are required from the ITS sequences.

Key words: biogeography, chloroplast genome, phylogeny, Quercus, unclear ITS