| Bainong64 has become one of the important parents of wheat breeding in the Southern Huang-huai wheat region because of its good disease resistance and wide adaptability. In this study, fluorescence in situ hybridization (FISH) and wheat 55K SNP chip analysis were used to analyze the whole genome of a total of 8 wheat varieties, including Bainong64 and its derivatives and related parents, to reveal the chromosome structural variation and the genetic contribution of Bainong64 to its derivatives. The results showed that a total of 48 polymorphic chromosome types (Blocks) were identified in this study wheat materials. The A, B and D genomes were 18, 20 and 10 blocks, respectively, of which 1A and 6B chromosome polymorphic types were the most. Pericentric inversion 6B (perInv6B) was identified in Bainong64 and its derivative Bainong207, and the wheat-rye translocation T1RS/1BL was identified in 5 cultivated wheat. Using the Affymetrix 55 K SNP chip, 8504, 9726 and 5093 polymorphic SNP markers were obtained in the A, B and D genomes of the tested materials, respectively. The polymorphism information content (PIC) ranged from 0.110 to 0.375, with an average of 0.295. The distribution of Bainong64-specific SNPs was 54.2 %, 46.9 % and 36.5 % on A, B and D genomes, respectively. The highest distribution was 85.4 % on chromosome 6A. The average distribution on each chromosome of Bainong207, Huayu198 and 04zhong 36 were more than 50.0 %. Integrated analysis of 48 blocks and 23,323 SNP markers showed that the genetic similarity coefficients (GS) of the derivatives and Bainong64 were more than 0.700 except for Bainong160. Cluster analysis showed that Bainong64 and its four derivatives were clustered into one group, which was consistent with the results of GS. It showed that Bainong64 had higher genetic contribution rate to its derivatives. This research provides a theoretical support for the utilization of wheat germplasm resources and parental selection in the breeding process.