The genetic basis of inbred line Huangzaosi and 14 Huanggaixi lines were analyzed by SNP Chips. Results showed that the similarity among inbred line Huangzaosi and 14 Huanggaixi lines was 90.1%-98.0%. The Huanggaixi lines had reached homozygous condition. Huanggaixi lines can be considered near-isogenic lines of inbred Huangzaosi. The similarity of 14 Huanggaixi lines in ten chromosomes was 88.3%-97.9%. In the process of breeding Huanggaixi lines, hybridity occurred on the ends of chromosomes where it was mutable and sensitive areas.