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Breeding endangered mammals for their conservation requires knowledge about the genetic architecture of the respective species. In taxa with tight genetic cohesion between populations, the definition of management units for captive breeding rarely poses problems, except if there are morphologically well differentiated subspecies grading into one another although they are hardly separate at the molecular level. Species with genetic diversity predominantly between populations can pose serious problems for breeders. Examples are discusses of mammalian species with complex genetic architectures, where decisions have to be drawn whether to select only certain populations for conservation, or to create an artificial taxon. Research into subspecific molecular taxonomy of rare zoo-living wildlife is frequently hampered by small sample sizes available for study, with the risk of spurious molecular taxonomic distances based on marker allele frequencies in populations influenced by genetic drift.