Chromosome genomics is the application of genomics tools to chromosomes. This approach greatly simplifies genome analysis in plants with large and/or polyploid genomes. The reduction of sample complexity is achieved by dissecting genomes to chromosomes via flow cytometric sorting. In bread wheat, this method has been used to develop markers from subgenomic regions, construction of sequence-ready physical maps of chromosome arms, map-based cloning and next generation sequencing. These efforts provide new insights into the structure and evolution of the polyploid genome and deliver tools to support wheat breeding. However, the narrow gene pool of bread wheat undermines the ability to sustain the crop yield and quality under extreme conditions. A solution is to involve wild relatives of wheat such as Aegilops, as donors of new alleles and genes in breeding via interspecific hybridization. However, despite extensive efforts, introgression of favorable agronomic traits from Aegilops to cultivated wheat remains difficult. Here we report on development of chromosome genomics in two wild diploid wheats, Ae. umbellulata and Ae. comosa, and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata. We have assessed a possibility to purify individual chromosomes by flow sorting and we have shot-gun sequenced to a high coverage by illumina chromosomes 1U, 3U and 6U of Ae. umbellulata and chromosome 1Ub of Ae. biuncialis. This provided first insights into to the sequence composition of Aegilops genomes, enabled assembly of low copy and genic regions and established syntenic relationship between the Aegilops chromosomes and genomes of brachypodium, rice, sorghum, barley and wheat.