Concerned that the island fox declines would lead to the extinction of the 3 island fox subspecies in the park, the National Park Service convened an Island Fox Recovery Team in April of 1999. This panel of experts identified golden eagle predation, parasites, and disease as serious threats to the fox's existence.

The captive-bred programs on neighboring Santa Cruz Island to the southeast and San Miguel Island to the west were shut down in 2007, their wild populations rebounding rapidly from near extinction. Their recovery appears to be one of the swiftest recoveries of an endangered species in the history of the Endangered Species Act.

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