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Note: The arrangement and nomenclature of orders, families, and genera are according to Simpson’s classification of 1945 (Bull. Am. Mus. Nat. Hist. (N. Y.), Vol. 85).
| Order INSECTIVORA—Moles and Shrews | ||||
| Family | Genus | Species | Subspecies | Common Name |
| SORICIDAE | Sorex | lyelli | Mount Lyell Shrew | |
| Sorex | trowhridgei | mariposae | Yosemite Shrew | |
| Sorex | vagrans | amoenus | Sierra Wandering Shrew | |
| Sorex | obscurus | obscurus | Dusky Shrew | |
| Sorex | palustris | navigator | Mountain Water Shrew | |
| TALPIDAE | Scapanus | latimanus | sericatus | Yosemite Mole |
| Order CHIROPTERA—Bats | ||||
| VESPERTILIONIDAE | Myotis | lucifugus | carissima | Yellowstone Little Brown Bat |
| Myotis | yumanensis | sociabilis | Tejon Bat | |
| Myotis | evotis | evotis | Little Long-eared Bat | |
| Myotis | thysanodes | Fringed Bat | ||
| Myotis | volans | longicrus | Long-legged Bat | |
| Myotis | californicus | californicus | Little California Bat | |
| Myotis | subulatus | melanorhinus | Black-nosed Bat | |
| Pipistrellus | hesperus | merriami | Merriam Canyon Bat | |
| Eptesicus | fuscus | bernardinus | San Bernardino Brown Bat | |
| Lasiurus | cinereus | cinereus | Hoary Bat | |
| Euderma | maculatum | Spotted Bat | ||
| Antrozous | pallidus | pacificus | Pacific Pallid Bat | |
| MOLOSSIDAE | Eumops | perotis | californicus | California Mastiff Bat |
| Tadartda | mexicana | mexicana | Mexican Free-tailed Bat | |
| Order LAGOMORPHA—Rabbits and their allies | ||||
| OCHOTONIDAE | Ochotona | princeps | muiri | Yosemite Cony or Pika |
| LEPORIDAE | Lepus | townsendi | townsendi | White-tailed Jackrabbit |
| Lepus | californicus | californicus | Black-tailed Jackrabbit | |
| Sylvilagus | bachmani | mariposae | Mariposa Brush Rabbit | |
| Order RODENTIA—Rodents or gnawing mammals | ||||
| APLODONTIDAE | Aplodontia | rufa | californica | Sierra Mountain Beaver |
| SCIURIDAE | Sciurus | griseus | griseus | California Gray Squirrel |
| Tamiasciurus | douglasi | albolimbatus | Sierra Chickaree | |
| Marmota | flaviventer | sierrae | Southern Sierra Marmot | |
| Citellus | beldingi | beldingi | Belding Ground Squirrel | |
| Citellus | beecheyi | sierrae | Sierra Ground Squirrel | |
| Citellus | lateralis | chrysodeirus | Sierra Golden-mantled Ground Squirrel | |
| Eutamias | alpinus | Alpine Chipmunk | ||
| Eutamias | speciosus | frater | Tahoe Chipmunk | |
| Eutamias | townsendi | senex | Allen Chipmunk | |
| Eutamias | quadrimaculatus | Long-eared Chipmunk | ||
| Eutamias | merriami | merriami | Merriam Chipmunk | |
| Glaucomys | sabrinus | lascivus | Sierra Flying Squirrel | |
| GEOMYIDAE | Thomomys | monticola | monticola | Sierra Pocket Gopher |
| Thomomys | bottae | mewa | Digger Pine Pocket Gopher | |
| Thomomys | bottae | awahnee | Yosemite Pocket Gopher | |
| HETEROMYIDAE | Perognathus | californicus | dispar | Allen Pocket Mouse |
| CASTORIDAE | Castor | canadensis | subauratus | Golden Beaver |
| CRICETIDAE | Reithrodoitomys | megalotis | longicaudus | Long-tailed Harvest Mouse |
| Peromyscus | maniculatus | gambeli | Gambel White-footed Mouse | |
| Peromyscus | boylei | boylei | Boyle White-footed Mouse | |
| Peromyscus | truei | gilberti | Gilbert White-footed Mouse | |
| Neotoma | fuscipes | streatori | Streator Wood Rat | |
| Neotoma | cinerea | acraia | Bushy-tailed Wood Rat | |
| Phenacomys | intermedius | celsus | Sierra Lemming Mouse | |
| Microtus | montanus | yosemite | Yosemite Meadow Mouse | |
| Microtus | californicus | mariposae | Mariposa Meadow Mouse | |
| Microtus | longicaudus | sierrae | Sierra Meadow Mouse | |
| MURIDAE | Rattus | rattus | alexandrinus | Roof or Alexandrine Rat |
| Mus | musculus | House Mouse | ||
| ZAPODIDAE | Zapus | pacificus | alleni | Allen Jumping Mouse |
| ERETHIZONTIDAE | Erethizon | dorsatum | epixanthum | Yellow-haired Porcupine |
| Order CARNIVORA—Flesh-eaters | ||||
| CANIDAE | Canis | latrans | lestes | Mountain Coyote |
| Vulpes | futva | necator | Sierra Red Fox | |
| Urocyon | cinereoargenteus | townsendi | Townsend Gray Fox | |
| URSIDAE | Ursus | americanus | californiensis | Sierra Black Bear |
| Ursus | horribilts | henshawi | Henshaw Grizzly Bear | |
| PROCYONIDAE | Bassariscus | astutus | raptor | California Ring-tailed Cat |
| Procyon | lotor | psora | California Coon | |
| MUSTELIDAE | Mustela | erminea | murica | Sierra Least Weasel |
| Mustela | frenata | nevadensis | Mountain Weasel | |
| Mustela | vison | energumenos | Pacific Mink | |
| Manes | americana | sierrae | Sierra Pine Marten | |
| Manes | pennanti | Fisher | ||
| Gulo | luscus | luteus | Southern Wolverine | |
| Taxidea | taxus | neglecta | California Badger | |
| Mephitis | mephitis | occidentalis | N. California Striped Skunk | |
| Spilogale | gractlis | phenax | California Spotted Skunk | |
| Lutra | canadensis | brevipilosus | California River Otter | |
| FELIDAE | Felis | concotor | californica | California Mountain Lion |
| Felis* | rufa | californica | California Wildcat | |
| Order ARTIODACTYLA—Even-toed, hoofed mammals | ||||
| CERVIDAE | Odocoileus | hemionus | hemionus | Rocky Mountain Mule Deer |
| Odocoileus | hemionus | californicus | California Mule Deer | |
| Odocoileus | hemionus | columhianus | Columbian Black-tailed Deer | |
| BOVIDAE | Ovis | canadensis | sierrae | Sierra Bighorn |
*Given as Lynx rufus californicus in most of the references listed in the bibliography.
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| Online Library: | Title | Author | California | Geology | History | Indians | Muir | Mountaineering | Nature | Management |
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