Patterns of genome variation in domestic animals have been shaped by the evolutionary and developmental process of domestication. Using whole-sheep genomes from a broad collection of domestic breeds and their wild ancestor the Asian mouflon (O.orientialis) we aim to assess the impact of domestication at a genome-wide scale. Following variant calling to identify approximately 45 million high confidence SNP, we find nucleotide diversity was generally higher in mouflon compared with their domesticated ancestors. To approach a deeper understanding of changing patterns of genomic diversity post domestication, we partitioned the sheep genome into 44 functional classifications. This utilised the current ovine annotation, sheep specific epigenomic datasets and human regulatory data (ENCODE and Epigenetics Roadmap) to predict the location of coding regions, promoters, enhancers and other elements of the gene regulatory machinery. Comparison of nucleotide diversity between functional classifications revealed coding regions contain the highest constraint, followed by promoters and finally enhancers. In addition, constraint within predicted promoters and enhancers is correlated to the number of tissues where they are active. Genomic regions that displayed marked reduction in diversity within domestic sheep, compared with the wild ancestors, were evaluated against each functional classification. We find strong evidence for enrichment for enhancer regions, suggesting a major consequence of domestication and selection has occurred in regulatory regions of the sheep genome. Currently, we are further characterizing these selective sweeps and their predicted consequences on gene expression.