Most of cultivated chrysanthemums (Chrysanthemum morifolium Ramat.) have been found to be polyaneuploid with hexaploid, 2n=6x=54, predominant. Cytological studies has shown that bivalent were normally formed and multivalent were rare during meiosis. These meiotic behavior reflected that the chromosome of chrysanthemum paired with its homologue preferentially and diploid-like inheritance was occurring. However, several genetic researches was in contrast to this hypothesis, based on the results of genetic analysis. Therefore, it is important to determine whether the mode of inheritance in chrysanthemum is disomic (selective pairing) or hexasomic (random pairing). ‘Dancer’ and ‘Puma White’, and their 94 crossing progenies were genotyped using 84 SSR primers. Alleles of each SSR locus were determined by length of PCR product with fluorescently labeled primers using ABI 3730 DNA Analyzer and GeneMapper 3.0 software (Applied Biosystems). A total of 210 types of alleles were detected in 49 SSR loci (4.29 allele types/locus). The observed segregation ratio of these alleles for 94 crossing progenies showed better fits to hexasomic than disomic. Moreover, based on the genotyping results, the genotypes of ‘Dancer’ and ‘Puma White’ were analyzed as BCDEFF and AACEEE in ChSSR-61 locus, respectively. And the genotypes of PD-33 and PD-51 were analyzed as ABDEEF and ABDEEF, respectively. It means that BDF alleles of PD-33 and BEE alleles of PD-51 were given from ‘Dancer’. If the chromosome is paired preferentially, the B allele would pair with C allele, D with E, and F with E at this locus of ‘Dancer’. But it was found PD-75 as AADEEF without B and C alleles. This is a clear evidence that the mode of inheritance in chrysanthemum is not disomic but hexasomic.