The bread wheat genome harbors a high content of repetitive DNA, which is amenable to detection and characterization using fluorescence in situ hybridization (FISH) karyotyping. An integrated genetic map was derived from a recombinant inbred population bred from a cross between a synthetic hexaploid wheat and a commercial Chinese bread wheat cultivar, based on 28 variable FISH sites and >150000 single nucleotide polymorphism (SNP) loci. The majority (20/28) of the variable FISH sites were physically located within a chromosomal region consistent with the genetic location inferred from that of their co-segregating SNP loci. The eight exceptions reflected the presence of either a translocation (1R/1B, 1A/7A) or a presumptive intra-chromosomal inversion (4A). For eight out of the nine FISH sites detected on the Chinese Spring (CS) karyotype, there was a good match with the reference genome sequence, indicating that the most recent assembly has dealt well with the problem of placing tandem repeats. The integrated genetic map produced for wheat is informative as to the location of blocks of tandemly repeated DNA and can aid in improving the quality of the genome sequence assembly in regions surrounding these blocks.