Pygmy marmosets are currently not endangered. However they are listed as special concern or somewhat threatened. Because of their size, mobility and coloration, it is almost impossible to count the pygmy marmosets living in the South American forests. A threat to these small monkeys is the pet trade.

The main predators of the pygmy marmoset are birds of prey. These monkeys are flexible and adapt to environmental changes caused by humans. For example, they have been found living in small groups of trees on the edges of farms that have been created by clear cutting. They have also been known to use secondary forest habitats if there is suitable food available.

As of April 2004, there are about 500 pygmy marmosets held in captivity throughout the world.

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