The DNA sequences of the internal transcribed spacer (ITS) region of the rRNA gene were determined in 20 taxa of 12 species of Fagopyrum. By comparing the sequence data and constructing phylogenetic trees, the phylogenetic relationships among the Fagopyrum species were established. The sequences of ITS (ITS1 and ITS2) were about 3-7 times more variable than those of the 5.8S subunit of the rRNA gene. The classification of Fagopyrum species based on the DNA sequences of the rRNA gene almost coincides with the classification based on morphology, allozyme variability, and nucleotide sequences of the rbcL-accD region of the chloroplast DNA. A close relationship of F. lineare with the F. statice-F. leptopodum clade was suggested and this was strongly supported by a 68-bp gap in ITS1 found in these three species. A tetraploid F. cymosum from Kathi, India, has two distinct rRNA genes probably on homoeologous chromosomes, and was distinguished from the clade of other diploid/tetraploid F. cymosum with a high bootstrap value. This strengthened the hypothesis of the polyphyletic origin of the tetraploid F. cymosum.