Wheat (Triticum aestivum L. 2n=6x=42; AABBDD) is the most widely grown crop worldwide and only recently has a completed genome sequence become available. However, a single genome assembly does not fully capture the genomic variation available for breeding and research. Here, we report highly contiguous assemblies of fifteen wheat cultivars and a spelt wheat landrace, as a step towards capturing the breath of genetic diversity currently utilized in global wheat breeding programs. For each cultivar, we assembled >14.2 Gb of sequence into 21 pseudomolecules with a scaffold N90s approaching 5 Mb. Systematic intergenomic comparisons with ancestral genomes of wild emmer wheat (AABB) and Aegilops tauschii (DD), the progenitors of the AABBDD genome of hexaploid wheat, revealed regions identical by descent since wheat domestication and other regions with acquired diversity contributing to adaptive features of wheat. For example, we characterized an approx. 30 Mbp telomeric segment on chromosome 2A corresponding to the “Vpm-1” introgression from Aegilops ventricosa that harbors critical genes for resistance to fungal rust pathogens. Population analysis of transposable elements across the three subgenomes revealed putative ancestral introgressions throughout the genome, with the strongest evidence on chromosomes 1A, 6A and 2D. We have projected wheat annotations onto our assemblies, and together with mapping of >30X coverage of 10X Genomics linked reads, we identified extensive presence/absence and copy number variation of genes across the 21 wheat chromosomes as well as single nucleotide variation in genes linked to key agronomic and end-use quality traits. Together with exhaustive RNASeq/IsoSeq across multiple tissues, this pan-genome of elite wheat cultivars and its comparison with ancestral genomes will shed light on the impact of past selections on global patterns of linkage disequilibrium and the genetic basis underlying key agronomic traits. Consequently, breeding programs will have improved resources for crop improvement, gene discovery, and future breeding efforts.