Many of the native species missing from the Shark Bay area are threatened or Endangered elsewhere in Australia. Some have survived only on isolated offshore islands. Consequently, captive breeding programs have been established for many of the animals needed for the reintroduction phase of Project Eden.

Colonies of bilbies, mala (rufous hare-wallaby), banded hare-wallabies, and western barred bandicoots are being bred at a special facility within Francois Peron National Park. These colonies are suplemented with animals from breeding programs at other agencies such as Perth Zoo (greater sticknest rat, Shark Bay mouse, chuditch) and Kanyana Wildlife Rehabilitation Centre (bilby, western barred bandicoot), as well as animals from interstate conservation programs (mala from NT; bilbies from NT and SA).

Peron Endangered Species Breeding Centre

Facilities and breeding enclosures were purpose-built in Francois Peron National Park in 1997-98 with funding assistance from Federal World Heritage funds and Coles 'Chocolate Bilby' donations via Environment Australia. World Heritage funding has continued to support the ongoing breeding programs each year since then.

Malleefowl were the first species to be raised at the centre, when wild collected eggs were artificially incubated and the hatched chicks reared at Peron in 1996, 97 and 98. Eggs were collected from the Wheatbelt region of WA and nearby populations in southern Shark Bay and Kalbarri, with the assistance of many local property managers. Sub-adult birds were subsequently released into the park in 1997-98.

The founding individuals for both western barred bandicoots and banded hare-wallabies were collected from Bernier Island