Abstract: The preparation method of DNA with high quality and low cost extracted from the slices of rice seeds was established for the high-throughput genotyping of breeding populations. The degree of purity and concentration of DNA extracted from the leaves of rice by TPS method and those of DNA extracted from the slices of rice seeds by using the method of 96-well plates combined with magnetic beads were compared in this paper. Then, the quality of DNA extracted from the slices of rice seeds by using the method of 96-well plates combined with magnetic beads was further verified by STARP (Semi-thermal asymmetric PCR) marker detection. The results showed that the quality and the degree of purity of DNA extracted from the slices of rice seeds by using the method of 96-well plates combined with magnetic beads were better than those of DNA extracted from the leaves of rice by TPS method. The verification results of STARP marker detection showed that the method of 96-well plates combined with magnetic beads to extract the DNA from the slices of rice seeds could be applied to the STARP marker genotyping of GS3 and Wx, and the identification results were consistent with the sequencing results. The results showed that the method of 96-well plates combined with magnetic beads could be used to extract the DNA with high recovery rate, high purity, high integrity and no PCR inhibitors from the trace slices of rice seeds for the analysis of gene haplotype with the high-throughput STATP method. Therefore, the operation flow of high-throughput genotyping for the DNA extraction by using the method of 96-well plates combined with magnetic beads could be obtained.