For sheep, more than 32 million single nucleotide polymorphisms (SNPs) have been discovered and 7K, 50K and 600K SNP chips and parentage SNP sets are available. For goats ~14.5 million SNP have been discovered and a 50K SNP chip is available. Application of the different chips and targeted genome resequencing allows imputation of the genome sequence of all individuals in a breed or population. Good quality annotated draft reference genome assemblies are also available for both species. Surveys of gene expression across a wide range of tissues have contributed to the construction of high quality gene models facilitating detailed analysis of the genes underlying traits. However, the current genome assemblies are not adequate for future applications. The focus of SNP discovery has now turned to the identification of causative mutations underlying traits. The resequencing of key individuals from a diverse range of breeds of each species, and of their undomesticated relatives, is enabling the exploration of the full extent of diversity within each species. Much of this diversity will be in regions of copy number variation (CNV), however, the imputation of CNV status is unlikely to be as successful as SNP alleles. New tools and resources, including improved assemblies of the reference genomes and alternate assemblies in CNV regions, and a better understanding of the relationship between the genome and the expression of the genes across the different tissues, will provide the foundation for a much broader utilisation of the sheep and goat genomic resources by their respective industries in the future. This work was partially supported by the EU FP7 3SR project (no. 245140).