Summary RAPD analysis was carried out using 60 random primers to investigate molecular genetic characterization of the amphidiploid Aster microcephalus var. ovatus and its presumable diploid parents. One of the presumable parents, A. iinumae, possesses S-type karyotype consisting of shorter chromosomes, which is considered to be derived from L-type karyotype consisting of longer chromosomes, characteristic to another presumable parent, A. ageratoides. In all, 611 reproducible fragments were amplified, and the fragment-band size range was from 50 to 12000 bp in the three species. Cluster analysis of RAPD data showed that the three species had quite similar genetic distances from each other with high values. The karyotypes of both Aster ageratoides and A. microcephalus var. ovatus include a set of L-type chromosomes, and the two species possess about 100 specific RAPD bands in common. The common band number between A. ageratoides and A. microcephalus var. ovatus was quite higher than those between A. ageratoides and A. iinumae, and between A. iinumae and A. microcephalus var. ovatus. This indicates that many fragments found in the L-type chromosomes do not exist in the S-type chromosomes, which could have caused chromosome size reduction from L-type to S-type.