Abstract: The purpose of this study is to explore elite alleles associated with seed storability from Japanica cultivars and typical carrier genotypes of these alleles. We investigated seed storability index of 100 Japanica cultivars from Taihu Lake area and Heilongjiang Province. 259 SSR markers were used to analyze the genome. The population analysis was conducted with Structure software. The association analysis between SSR markers and seed storability was conducted with general linear model. The phenotypic mean of the material with null allele was as the control, the carrier with elite allelic variation was detected. (1) The seed storability and the genetic diversity of Taihu Lake area Japanica cultivars were higher than that of Heilongjiang Province. (2) There were 71 SSR markers associated with the seed storability at all. Seventeen SSR markers associated with seedling height were detected, RM6811 had the maximum contribution rate (50.54% ). The biggest allelic variation of the increasing phenotypic effect was RM5753-215, the carrier variety was‘Taijing16haoxuanzi’. Twenty-six SSR markers associated with root length were detected, RM5753 had the biggest contribution rate (49.3%), the biggest allelic variation of the increasing phenotypic effect was RM5753-207, the carrier variety was‘Kendao2hao’. Twenty- eight SSR markers associated with dry weight were detected, RM5340 and RM24481 had the biggest contribution rate (50.49% and 50.51%, respectively), the biggest allelic variation of the increasing phenotypic effect was RM180-101, the carrier variety was‘Lianjing4hao’.