Field Guide to the Lost Species of the San Francisco Bay Area

October 1, 2007

If you look up any of the lost species featured in the pages of our October-December 2007 feature Presumed Extinct, you’re likely to find just that—the words presumed extinct followed by a brief natural history account, if you’re lucky. In the hope that these lost species might someday become Lazarus species—plants and wildlife that rise up from the dead—we’ve put together a field guide to help Bay Area naturalists in their search for the next Holy Grail.

While the likelihood of finding a lotis blue butterfly or Pitkin Marsh Indian paintbrush in your backyard or on a weekend hike are slim-to-none (both are restricted to private property), there’s no reason why a mail carrier might not stumble across a Palo Alto lost thistle on her way to the post office, or an itinerant hiker might not hit upon a Strohbeen’s Parnassian butterfly in the Santa Cruz Mountains. Or, realistically, why it’s worthwhile to reach for your field guide the next time your housecat leaves a present on the doorstep—it could be a Berkeley kangaroo rat! And then there’s Rich Mooi’s offer to those interested in visiting the California Academy of Sciences to learn about the Bay’s benthic creatures, a free ticket to paw through jars of mud in search of the San Francisco horseshoe shrimp. So read up; we’re counting on you to keep your eyes peeled!

SPECIES: Strohbeen’s Parnassian butterfly (Parnassius clodius strohbeeni)



RANGE: known only from the Santa Cruz Mountains in Santa Cruz County

HABITAT: host plant is western bleeding heart (Dicentra formosa); redwood forests, well-lit canyon bottoms, stream zones

FIELD NOTES: of the Parnassian butterflies (P. clodius), Strohbeen’s Parnassian is a lighter sub-species restricted to the Santa Cruz Mountains; its closest cousins are found in the high inner North Coast Range, the Klamath Mountains, and the west slope of the Sierra Nevada; the Strohbeen’s Parnassian’s flight period is late May to early July


Field Guide to Butterflies of the San Francisco Bay and Sacramento Valley Regions, by Arthur M. Shapiro and Timothy D. Manolis

Lotis blue butterfly
Lotis blue butterfly (Lycaeides idas lotis). Illustration by DevinCecil-Wishing.”


SPECIES: lotis blue butterfly (Lycaeides idas lotis)

LISTING STATUS: federally endangered


RANGE: scattered locations throughout Mendocino and Sonoma County; last known from a single location on PG&E land in Mendocino County’s Pygmy Forest

HABITAT: suspected host plant is seaside bird’s-foot trefoil (Lotus formosissimus); wet meadows, spagnum-willow bogs

FIELD NOTES: the lotis blue is often described as a larger version of its fellow blue, the Melissa blue butterfly (Lycaeides melissa); the lotis blue’s flight period is mid-April to June


Field Guide to Butterflies of the San Francisco Bay and Sacramento Valley Regions, by Arthur M. Shapiro and Timothy D. Manolis

Lotis Blue Draft Recovery Plan, March 13, 1996, by the U.S. Fish and Wildlife Service

Clear Lake splittail
Clear Lake splittail (Pogonichthys ciscoides) illustration byDevin Cecil-Wishing.

SPECIES: Clear Lake splittail (Pogonichthys ciscoides)



RANGE: known only from Clear Lake in Lake County

HABITAT: Clear Lake and its tributary waters, plus an outlying record from Cache Creek (downstream of Clear Lake)

FIELD NOTES: a lake-bound cousin of the Sacramento splittail (P. macrolepidotus), Clear Lake’s shoreline splittail wasn’t officially described until 1973, approximately the time it went extinct; aside from geographic isolation, the differences between the species are morphological; compared to the Sacramento splittail, the Clear Lake splittail has more gill rakers, more lateral line scales, smaller fins, a terminal mouth with absent or reduced barbels, and a relatively symmetrical tail fin


Inland Fishes of California, by Peter B. Moyle

Field Guide to Freshwater Fishes of California, March 13, 1996, by Samuel M. McGinnis

SPECIES: thicktail chub (Gila crassicauda)


FIRST/LAST RECORDED: present in Native American middens/1957

RANGE: reported specifically in Sacramento River, Putah Creek, Pajaro-Salinas drainage, Clear Lake, San Francisco Bay, Coyote Creek, Central Valley lowlands, and Bay tributary streams

HABITAT: lowland lakes, sloughs, slow-moving river stretches, and surface waters of the San Francisco Bay

FIELD NOTES: thicktail chub remains are reportedly common in Native American middens along the Sacramento River, and have been recovered from 19th-century Chinese privies in San Francisco’s Mission District; in the 19th century the fish was commonly sold in San Francisco fish markets and was served in Sacramento saloons; compared to other chub, the thicktail chub is a heavy-bodied fish with a small, cone-shaped head, greenish brown to purplish black back, and yellowish sides and belly


Inland Fishes of California, by Peter B. Moyle

Field Guide to Freshwater Fishes of California, March 13, 1996, by Samuel M. McGinnis

Shasta crayfish
Illustration based on Shasta crayfish photo by B. Moose Peterson/WRP

SPECIES: sooty crayfish (Pacifastacus nigrescens)


FIRST/LAST RECORDED: 1857/late 1800S

RANGE: reported specifically in Alameda Creek, Coyote Creek, Steamboat Slough, and other Bay tributary streams

HABITAT: freshwater Bay tributary streams

FIELD NOTES: the sooty crayfish hasn’t been seen in over 100 years; the sooty crayfish closely resembles its cousin the Shasta crayfish (Pacifastacus fortis) but is blackish, smaller in size (4 inches long), and has more slender, hairless hands (claws)


Crayfishes (Astacidae) of North and Middle America, by Horton H. Hobbs

Ask the Naturalist—All the Crawdads You Can Eat (Bay Nature), March 13, 1996, by Michael Ellis

SPECIES: San Francisco horseshoe shrimp (Lightiella serendipita)



RANGE: known only from San Francisco Bay at Point Richmond, Brooks Island, Coyote Point

HABITAT: muddy sand bottom

FIELD NOTES: although extensive sampling has been done to rediscover this shrimp at its type locality and other collection locations, “searching” for this species amounts to sorting through Bay mud; mud-raker Richard Mooi of the California Academy of Sciences has generously offered would-be shrimp seekers the opportunity to pick through jars of mud—with the proper training, of course—to make sure no horseshoe shrimp have been overlooked— Reach Mooi at (415)321-8270.

Horseshoe shrimp
San Francisco horseshoe shrimp (Lightiella serendipita)illustration by Devin Cecil-Wishing.


Animals of San Francisco Bay: A Field Guide to Its Common Benthic Species, by Rich Mooi, Victor G. Smith, Margaret Gould Burke, Terrence M. Gosliner, Christina N. Piotrowski, and Rebecca K. Ritger

SPECIES: Palo Alto lost thistle (Cirsium praeteriens)

LISTING STATUS: CNPS List 1A (presumed extinct in California)


RANGE: known only from Palo Alto in Santa Clara County

HABITAT: unknown

FIELD NOTES: with nothing but “Palo Alto” recorded for the type specimen’s collection location, botanists know nothing about this thistle’s preferred habitat; notes to the effect that the species represents an introduction from the Old World are unsubstantiated and the species is still recognized today as a native California thistle

Palo Alto lost thistle (Cirsium praeteriens) illustration by DevinCecil-Wishing


CNPS Inventory of Rare and Endangered Plants of California, Online Edition, 2007, by the Rare Plant Scientific Advisory Committee, California Native Plant Society

Digitized type specimen at Harvard University Herbarium Index of Botanical Species

Flora of North America, Flora of North America Committee

Indian paintbrush

Pitkin Marsh Indian paintbrush (Castilleja uliginosa) illustrationby Devin Cecil-Wishing.”

SPECIES: Pitkin Marsh Indian paintbrush (Castilleja uliginosa)

LISTING STATUS: state Endangered; CNPS List 1A (presumed extinct in California)


RANGE: Pitkin Marsh, Trembley’s Marsh in Sonoma County

HABITAT: marshy meadows

FIELD NOTES: the Pitkin Marsh Indian paintbrush grows solely in association with rhododendron plants in a type of hemiparasitic relationship; all known plants were reported on private land, which has prevented further surveys to determine if any unrecorded plants have persisted


Indian Paintbrush: The Sunset Shades of Castilleja (Bay Nature), by Geoffrey Coffey

CNPS Inventory of Rare and Endangered Plants of California, Online Edition, 2007, by the Rare Plant Scientific Advisory Committee, California Native Plant Society

Kangaroo rat
Illustration based on photo by Dr. Lloyd Glenn Ingles, (c) California Academy of Sciences

SPECIES: Berkeley kangaroo rat (Dipodomys heermanni berkeleyensis)

LISTING STATUS: Species of special concern


RANGE: Berkeley (Strawberry Canyon), Mt. Diablo, and the East Bay Hills (Orinda Park Pool, Siesta Valley, Calaveras Reservoir)

HABITAT: bare ridge tops, rocky outcrops, thin soils, scattered chaparral, and small annual grasses

FIELD NOTES: the Berkeley kangaroo rat closely resembles the Tulare kangaroo rat (D. h. tularensis), but can be distinguished by generally darker hairs, especially along the back, as well as darker broad stripes along the sides and tail, and smaller patches of lighter hairs on the ears and face; look for k-rat hunter Gary Beeman’s “Wanted!” posters in kiosks surrounding Mount Diablo State Park; if you want to tip off Beeman about a potential k-rat in your neighborhood, you can reach him at (925)284-2602


Draft Recovery Plan for Chaparral and Scrub Community Species East of San Francisco Bay, California, by the U.S. Fish and Wildlife Service



The California Department of Fish and Game maintains regularly updated lists of the state’s special-status plant and animal species, from high-profile threatened and endangered species to “species of special concern,” whose populations are dwindling and may warrant state or federal listing action in the future.

Special Vascular Plants, Bryophytes, and Lichens List (.pdf)

Special Animals List (.pdf)

Endangered, Threatened, and Rare Plants List (.pdf)

Endangered and Threatened Animals List (.pdf)

Fully Protected Animals List(.pdf)

Fish Species of Special Concern List (.pdf)

Amphibian Species of Special Concern List (.pdf)

Reptile Species of Special Concern List (.pdf)

Bird Species of Special Concern List (.pdf)

Mammal Species of Special Concern List (.pdf)


Jepson Online Interchange for California Floristics, Jepson Flora Project

CalFlora Database

CNPS Inventory of Rare and Endangered Plants of California, Online Edition


The U.S. Fish and Wildlife Service and the California Department of Fish and Game aren’t the only agencies working to protect and conserve species and their habitat. There are many organizations and institutions that devote time, money, and resources to research and conservation efforts on behalf of plants and wildlife in the Bay Area, not to mention world-wide. Those whose goals and sphere of influence overlap with the Bay Area’s lost species are listed below:


Butterfly Organizations

Entomological Society of America

Lepidopterists’ Society

North American Butterfly Association

Xerces Society

Young Entomologists’ Society

The Pacific Coast Entomological Society

North American Pollinator Protection Campaign

The Pollinator Partnership

Plant Organizations

California Native Plant society

Crustacean Organizations

The Crustacean Society

Wildlife Organizations

The Wildlife Society

Land Trusts

Solano Land Trust

UC Natural Reserves [Jepson Prairie Preserve]

Presidio Trust

Lake County Land Trust

Sonoma Land Trust

Save Mount Diablo


California Academy of Sciences, San Francisco

Museum of Vertebrate Zoology, Berkeley

Museum of Comparative Zoology, Harvard University

American Museum of Natural History, New York

Essig Museum of Entomology, Berkeley

Herbaria & Botanical Gardens

University of California Botanical Garden at Berkeley

Regional Parks Botanic Garden

San Francisco Botanical Garden at Strybing Arboretum

The University and Jepson Herbaria

Herbarium of the California Academy of Sciences

Harvard University Herbaria


The inspiration behind “Presumed Extinct: Lost Species of the Bay Area” was the rediscovery of the Bay Area”s own ivory-billed woodpecker, the Mount Diablo buckwheat. You can learn more about Mount Diablo and its phantom buckwheat through the following features and press releases:

Bay Nature Magazine

Speak of the Devil: The Unexpected Landscapes of Mount Diablo

The Mount Diablo Buckwheat One Year Later

Save Mount Diablo

Press Release: “Mt. Diablo Buckwheat Rediscovered”

California State Parks

News Release: Wildflower Back from Extinction After 69 Years—U.C. Berkeley Propogates Rare Plant Discovered at Mt. Diablo State Park (.pdf)


When so-called “extinct” species rise from the dead—as we hope our lost Bay Area species are fated to do—they become what are appropriately referred to as “Lazarus species.” You can learn more about such species and how they become extinct, as well as test your knowledge on global extinction—through the links below:

“How are species classed as extinct?”

Attenborough’s Long-Beaked Echidna—”New hope over ‘extinct’ echidna”

White Dolphin “baiji”—White Dolphin Appears from the Brink

Manipur Bush-Quail—”‘Extinct’ quail sighted in India”

Giant Capricorn Beetle—”Carpenter finds ‘extinct’ beetle”

Painted Frog—”‘Extinct’ frog comes back to life”

Tasmanian Tiger—”Hunting Tasmania’s extinct ‘tiger'”

New Zealand Storm Petrel—”NZ seabird returns 150 years on”

“Quiz: Species and extinction”

About the Author

Matthew Bettelheim is a freelance writer and a wildlife biologist with URS Corporation.

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