Abstract: The purpose of this study were to detect elite alleles associated with anaerobic tolerance of seedling from japonica rice varieties growing in Taihu Lake region, and to screen typical carrier genotypes of these alleles. The genotyping data of 91 simple sequence repeat (SSR) markers on representative samples of 94 varieties were used in the present study, and the anaerobic responsive index of seedling were investigated. The association analysis between SSR loci and the anaerobic tolerance was performed using General Linear Model program in Tassel 2.0. Elite alleles and their carrier materials were determined on the basis of the result of comparisons between the average phenotypic value of accessions with the specific allele and that of accessions with “null allele”. Four SSR loci associated with seedling anaerobic tolerance were detected. Six elite alleles were RM311-176bp, RM317-164bp, RM112-127bp, RM20-205bp, RM317-157bp, and RM311-170bp. Zhendao88, Baimangnuo, Kaiqing Youmangzaodao, Cuganhuangdao and C-bao were carrier genotypes having the elite alleles for seedling anaerobic tolerance.