Recently developed genomic tools, like SNP-genotyping and whole genome sequencing, and their analysis, offer great opportunities for the conservation and utilisation of animal genetic diversity, both among and within breeds. These genomic tools can be used to detect potentially valuable rare alleles and haplotypes. They are important parts of the genetic diversity we need to conserve now for possible utilisation in the future. This book describes the use of genomic technology to define breeds, to measure diversity and to assess important features in the history of breeds affecting the present genetic diversity. The management of genetic diversity with genomic tools is outlined both in vivo: small populations of rare breeds or large populations with small effective population sizes and in vitro: genebanks. Special attention is given to the genomic management of populations of animals with high incidences of genetic defects. This book is intended for MSc and PhD students, scientists working with small populations in animal breeding and in conservation programmes for rare breeds.