The distribution of recombination events along large cereal chromosomes is uneven and generally restricted to gene-rich telomeric ends. In order to understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 cultivars, landraces, and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared to wild barley. We observed a mixture of completely and partially differentiated SNPs between domesticated and wild genepools, suggesting the former were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. While most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated 2-row and 6-row types associated with different geographical origins. Within the pericentromeric regions we identified 22,387 non-synonymous SNPs, of which 92 were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be 'highly deleterious'. . Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools with different evolutionary processes driving domestication and diversification.