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There are currently two levels of breeding programme: European Endangered Species Programme (EEP), and the European StudBook (ESB). Each EEP is coordinated by a member of staff within member institutions, while the ESB will have an individual Stud book holder.

These specialist programmes aim to maintain and conserve healthy populations within zoos, while also protecting the genetic health of many vulnerable species, and zoos taking part in them collaborate to exchange individual animals in order to achieve the best genetic combinations to breed together. For many species.

EAZA actively promotes the protection of threatened natural habitats through campaigns and community education initiatives often involving member zoos and aquariums, and for many species managed through breeding programmes, their native habitats are the subject of in situ education and conservation work.