Using meiosis and mitosis chromosomes, we have karyotyped and physically mapped of Humulus japonicus. The somatic metaphase chromosome numbers were 2n = 2x = 14 + XX in female, 2n = 2x = 14 + XY1Y2 in male and 2n = 3x = 21 + XXX in triploid. The 5S and 45S rDNA genes were physically mapped on the metaphase chromosomes using fluorescence in situ hybridization (FISH). One pair of 5S rDNA gene was detected on the short arm of chromosome 4 and two pairs of 45S rDNA gene were observed on the terminal regions of the short arms of chromosome 5 and 7 in both female and male plants. In addition, three pairs of two rDNAs were detected on the chromosome 4, 5 and 7 of triploid. At meiosis, a trivalent chromosome figure was clearly seen, of which Y1 and Y2 could be distinguished from X by their premature condensation and three chromosomes, Y1-X-Y2, the forms associated by terminal chiasmata.