It depends on the zoo. To breed animals responsibly, a zoo should be a member of the Association of Zoos and Aquariums (in North America. There are similar programs in different parts of the world). This association coordinates which members of a given species should mate with which others to prevent inbreeding and maintain diversity. When breeding is recommended, one of the animals is shipped to the other, to whichever zoo is better able to provide conditions for mating. In this way, species that are nearly or completely extinct in the wild can maintain the healthiest possible populations in captivity.
Within the zoos, genetic diversity can indeed decrease due to inter-breeding. However, if the zookeepers are careful, genetic diversity can be maintained. It can be difficult to maintain the genetic diversity of endangered animals due to the lack of animals available for breeding, and high infant mortality can ensue as a result.
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