Sequence elimination is one of main reasons for homologous chromosome differentiation in common wheat. Sequence elimination can occur in genome-specific sequences, chromosome-specific sequences, and repeat sequences in the wheat genome. Genetic polymorphism loci in chromosome-specific sequences can be used to develop molecular markers including simple sequence repeats (SSRs), insertions and deletions, and single nucleotide polymorphisms (SNPs). Pubing3504 is a wheat-Agropyron cristatum (L.) Gaertn introgression line, and Jing4839 is a common wheat cultivar. Assessment of their recombinant inbred line (RIL) population using 120 pairs of SSR markers covering all wheat chromosomes indicated that sequence elimination occurred at the short arm of chromosome 1A (1AS). We developed 13 pairs of new co-dominant SSR markers and constructed a genetic linkage map of 1AS; we found that the segment with sequence elimination is from SSR110 to the end of 1AS. We further developed 10 pairs of dominant SNP markers of Pubing3504, 10 pairs of dominant SNP markers of Jing4839, and 10 pairs of primers designed in SNP flanking sequences to assess RILs. We found that all chromosome segments with sequence elimination came from Jing4839. The sequence elimination occurred in SSR loci, SNP loci, and coding sequences. There was no homologous recombination in the chromosome segment with sequence elimination. We suggest that sequence elimination causes the differentiation of chromosomes and the chromosome differentiation affects the homologous pairing at the chromosome segment in meiosis, which further affects the occurrence of homologous recombination at the chromosome segment.