DoD Biodiversity Conservation Handbook
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Chapter 6 Case Studies

Endangered Species: San Clemente Island

Management of Threatened, Endangered and At-Risk Species

San Clemente Island (SCI) is the southernmost of the eight California Channel islands. It lies 55 nautical miles (nm) south of Long Beach and 68 nm northwest of San Diego. The island is approximately 21 nm long and is 4.5 nm across at its widest point. Since 1934, the island has been owned and operated by various U.S. naval commands. A dozen range and operational areas are clustered within a 60-mile radius of the island as part of the Southern California Offshore Range Complex. The Commander, Naval Forces Pacific, is the major claimant for the island, and Naval Base Coronado is responsible for its administration. For additional information, see the following web sites:

Biological Significance

SCI possesses a remarkable biological diversity, including many endemic species and ten species that are federally listed as either endangered or threatened:

  • SCI loggerhead shrike (Lanius ludovicianus mearnsi)
  • Western snowy plover (Charadrius alexandrinus nivosus)
  • Sage sparrow (Amphispiza belli clementeae)
  • Island night lizard (Xantusia riversiana)
  • SCI rock cress (Sibara filifolia)
  • SCI bushmallow (Malacothamnus clementinus)
  • SCI Indian paintbrush (Castilleja grisea)
  • SCI broom (Lotus dendroideus ssp. Traskiae)
  • SCI larkspur (Delphinium kinkiense)
  • SCI woodland star (Lithophragma maxima)

Also, the island harbors the island fox, a species that occurs on five other Channel islands, but which is a species of concern on SCI.

Management of Listed Species

  • In the 1970s the Navy recognized that recovering listed species on the island would not be possible without the removal of feral goat and pig populations, which negatively impacted the entire native biota. By 1991, all feral goats and pigs had been removed from the island.
  • There are currently five separate Biological Opinions (BO) rendered by the U.S. Fish and Wildlife Service (USFWS) under the authority of the Endangered Species Act.
  • The terms and conditions from these bos have been translated into conservation actions and/or goals in the SCI Integrated Natural Resources Management Plan (INRMP).
  • The INRMP also identified areas on the island with high and low inherent military value, and high and low inherent natural resources values. Most conservation efforts are focused on those parts of the island where high military and high natural resources values overlap, such as at the extreme ends of the island, thereby reducing conflicts.

Management of Species at Risk

  • The island fox, which is experiencing declines on other Channel islands, could be listed at SCI.
  • To obviate listing, the Navy has worked with the USFWS to eliminate major threats to the island fox population:
  • Development of non-lethal fox deterrents to protect the endangered loggerhead shrikes from predation
  • Reducing road kills
  • In 2003, the Navy entered into a cooperative conservation agreement with the USFWS to develop an island fox management plan.
  • Also in 2003, the Navy nominated the island fox to the dod Legacy Species at Risk Program. Through the program, implemented by the conservation organization NatureServe, a management plan for the SCI fox was developed cooperatively among Navy biologists, the USFWS, and the State of California Natural Heritage Program. Visit the following web site for more details:


  • The removal of feral animals has allowed for the recovery of native vegetation, which has significantly enhanced habitat for most other animal species, especially the SCI loggerhead shrike.
  • A restoration program is enhancing habitats for endangered species by augmenting
  • the distribution of native plants propagated in the island's nursery. To date, thousands of individuals have been planted, with a survival rate at about 90 percent.
  • There have been no interruptions of the Navy's training and testing activities on SCI due to threatened, endangered, or sensitive species.
  • The island night lizard population may soon be de-listed by the USFWS.
  • Navy-sponsored population studies on the San Clemente sage sparrow have revealed valuable data for the development of recovery strategies for the species.

Lessons Learned

  • Fostering good working relationships with federal regulatory agencies, in this case the USFWS, increases management options for the conservation and recovery of endangered species.
  • By openly sharing operational training requirements and an assessment of associated impacts with federal regulatory agencies, trust is enhanced. Over at least a decade of coordination between the Navy and USFWS, the latter has gained both an understanding and an appreciation for the military mission at sci, and for the Navy's commitment to environmental stewardship.
  • Environmental stewardship must be proactive, such as the identification of and the application of management strategies for species of concern prior to their listing. The island fox candidate conservation agreement with the USFWS, implemented through the Legacy-funded Species at Risk Program sponsored by NatureServe, will both protect the population and obviate its listing.


San Clemente Island supports some of the most important weapons research, development, test, and evaluation programs and essential military operational training within the Navy. Despite such activity, the island's biological community is being both preserved and enhanced through multiple natural resources conservation and management programs. The Navy, in cooperation with the USFWS and other governmental environmental agencies, and with the support and encouragement of nongovernmental environmental organizations, such as The Nature Conservancy and NatureServe, has been able to achieve to the maximum extent possible both the military mission and environmental stewardship in a setting unique to each.

© Copyright 2008. NatureServe.

About This Case Study's Author
By Luis Perez
Installation Environmental Program
Naval Base Coronado
Phone: 619-545-3429

NatureServe DoD