The priority of animal breeding in organic agriculture lies with the improvement of functional traits (health, fertility and longevity) and product quality. This will be achieved through adaptive breeding strategies with special emphasis on genetic diversity. Applied methods of statistical animal genetics, such as lifetime analyses and the analysis of health traits must be continuously improved and adapted to the various practical questions. In addition to phenotypes and pedigrees of animals, genomic information must be incorporated in breeding value estimation and breeding plan calculations. This offers new possibilities for animal breeding and management of genetic diversity in organic agriculture. Moreover, special aspects such as genotype by environment interactions are challenges for finding the optimized breeding strategy for organic farming.