A physical map is a prerequisite for the sequence assembly of large genomes such as that of wheat (Triticum aestivum L). We are constructing physical maps of fraction-I, flow-sorted chromosomes 1D, 4D, and 6D of the hexaploid wheat Chinese Spring (CS). Three BAC libraries from CS fraction I with 15.3x chromosome coverage were developed, and 280,000 BAC clones from EcoRI and HindIII BAC libraries were fingerprinted with SNaPshot HICF technology. High-quality fingerprints of 200,000 BAC clones were assembled into 5,162 contigs as a first draft assembly of the CS fraction I. A minimum tiling path of 34,350 clones was refingerprinted with a technique and instrumentation identical to those previously used for fingerprinting the Aegilops tauschii BAC libraries. The fraction-I and Ae. tauschii fingerprints were combined into a single database and contigs were assembled. The co-assembly revealed relationships between most of the fraction-I contigs and Ae. tauschii contigs and anchored the CS contigs on the Ae. tauschii physical map. Five-dimensional, random BAC pools and three-dimensional MTP BAC pools were developed by pooling 92,160 and 34,350 clones, respectively. A 10K Illumina Infinium SNP assay designed from Ae. tauschii sequences is being used to develop a high-density genetic map using a wheat x synthetic RIL population of 188 F6 individuals and anchoring BAC contigs on the wheat and Ae. tauschii genetic maps. Progress on the development of integrated genetic and physical maps of wheat chromosomes 1D, 4D, and 6D and their integration with the Ae. tauschii physical map will be presented.