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. They recommended the park take the following measures to help bring the fox back from the brink of extinction:

• Start a captive breeding program to protect remaining foxes from mortality, and increase critically low fox populations (2005 Fox Recovery Report);
• Capture golden eagles on the northern islands and relocate them to suitable habitat on the mainland;
• Restore bald eagles to help displace golden eagles;
• Seek to have the island fox listed as an endangered species;
• Remove feral pigs from Santa Cruz Island

In 1999 the 15 remaining foxes on San Miguel Island were brought into captivity. The following year, the NPS brought the remaining 14 Santa Rosa Island foxes into captivity. By 2004 those captive populations had grown to 38 and 54 foxes respectively. To date, 32 golden eagles have been captured and relocated by the Santa Cruz Predatory Bird Research Group from Santa Cruz Island. An unknown number, possibly less than 10, remain on the island.

Beginning in June, 2002, bald eagles are being restored to Santa Cruz Island by the Institute for Wildlife Studies with funding from the Montrose Settlement. Up to 12 chicks per year will be released from hack boxes on the island. The U.S. Fish and Wildlife Service listed the four northern subspecies of island fox as endangered in 2004.

In 2003 NPS released its Conservation Strategy for Recovery of Island Foxes (2 mb .pdf) on the northern Channel Islands. Written in the format of a USFWS recovery plan, the strategy presents a road map for recovery of Island Foxes on Santa Cruz, Santa Rosa, and San Miguel slands.