The male and female trees of Ginkgo biloba can only be distinguished by studying the morphology of reproductive organs. This study was undertaken to investigate the chromosomal differences between the sexes of this dioecious species. The somatic chromosome number of the male and female trees is 24 (2n=24). The difference in the karyotype of the male and female trees was observed in the number of satellite chromosomes. There were three in the male and four in the female trees. The satellites were observed on the two largest metacentric chromosomes in both male and female trees, whereas only one sub-metacentric chromosome in the male and two sub-metacentric chromosomes in the female tree. Chromosomes stained with chromomycin A₃ (CMA), exhibited yellow bands near the terminal of the short arms of the two largest metacentric chromosomes and the long arms of two sub-metacentric chromosomes in the male as well as the female trees. Utilizing fluorescence in situ hybridization (FISH) analysis with rDNA as probe, the signals were observed at the same four positions in both the male and female trees. Hence, the discrimination of male and female trees at the chromosome level can only be made on the basis of the number of satellites.