Inheritance of SSR markers, linkage arrangement of the SSR loci and genotyping of asparagus cultivars of different ploidies were investigated. The segregation patterns of SSR markers in the progenies of 'Hokkai 100' × 'UC157F1', 'Welcome' × 'Welcome' and 'Gold Schatz' × 'Hokkai 100' fitted with Mendelian inheritance in six EST-SSR loci, AG2, AG3, AG7, AG10, TC1 and TC7. One linkage combination of 'Asp1-T7sp marker (Nakayama et al., 2006), AG3' was recognized with the recombination fractions of 0.138 at 1% level. There were 34 alleles in the six loci ranging from four to eight alleles per locus. SSR genotypes of diploid, triploid and tetraploid cultivars were distinguished, and parental genotypes of the diploid clonal hybrid cultivars were estimated from their segregation patterns.