| Genus | Species | Common Name | Synonyms |
| Soricidae Shrew Family | |||
| Notiosorex | crawfordi | Desert Shrew | Gray Shrew |
| Scapanus | latimanus | Broad-footed Mole | |
| Vespertilionidae Vesper Bat Family | |||
| Antrozous | pallidus | Pallid Bat | |
| Laziurus | cinereus | Hoary Bat | |
| Myotis | californicus | California Myotis | |
| Myotis | ciliolabrum | Western Small-footed Myotis | M. subulatus |
| Myotis | volans | Long-legged Bat | |
| Pipistrellus | hesperus | Western Pipistrelle | |
| Leporidae Rabbit and Hare Family | |||
| Lepus | californicus | Black-tailed Jackrabbit | |
| Sylvilagus | audubonii | Desert Cottontail | |
| Sylvilagus | bachmani | Brush Rabbit | |
| Sciuridae Squirrel Family | |||
| Ammospermophilus | leucurus | White-tailed Antelope Squirrel | |
| Neotamias | merriami | Merriam Chipmunk | Eutamias m., Tamias m. |
| Sciurus | griseus | Western Gray Squirrel | |
| Spermophilus | beecheyi | Beechey Ground Squirrel | California Ground Squirrel |
| Spermophilus | tereticaudus | Round-tailed Ground Squirrel | |
| Geomyidae Pocket Gopher Family | |||
| Thomomys | bottae | Botta’s Pocket Gopher | |
| Heteromyidae Pocket Mouse and Kangaroo Rat Family | |||
| Chaetodipus | baileyi | Bailey’s Pocket Mouse | Perognathus b. |
| Chaetodipus | fallax | San Diego Pocket Mouse | Perognathus f. |
| Chaetodipus | formosus | Long-tailed Pocket Mouse | Perognathus f. |
| Chaetodipus | penicillatus | Desert Pocket Mouse | Perognathus p. |
| Chaetodipus | spinatus | Spiny Pocket Mouse | Perognathus s. |
| Dipodomys | agilis | Nimble Kangaroo Rat | |
| Dipodomys | deserti | Desert Kangaroo Rat | |
| Dipodomys | merriami | Merriam’s Kangaroo Rat | |
| Perognathus | longimembris | Little Pocket Mouse | |
| Cricetidae Deer Mouse and Woodrat Family | |||
| Microtus | californicus | California Vole | |
| Neotoma | lepida | Desert Wood Rat | Desert Pack Rat |
| Onychomys | torridus | Southern Grasshopper Mouse | |
| Peromyscus | boylii | Brush Mouse | |
| Peromyscus | californicus | California Mouse | |
| Peromyscus | crinitus | Canyon Mouse | |
| Peromyscus | eremicus | Cactus Mouse | |
| Peromyscus | maniculatus | American Deer Mouse | |
| Peromyscus | truei | Pinyon Mouse | |
| Muridae Old World Rats and Mice | |||
| Mus | musculus | House Mouse | |
| Rattus | rattus | Roof Rat | Black Rat |
| Canidae Wolf and Fox Family | |||
| Canis | latrans | Coyote | |
| Urocyon | cinereoargenteus | Common Gray Fox | |
| Vulpes | macrotus | Kit Fox | |
| Procyonidae Raccoon Family | |||
| Bassariscus | astutus | Ringtail | |
| Procyon | lotor | Northern Raccoon | |
| Mustelidae Weasel Family | |||
| Mephitis | mephitis | Striped Skunk | |
| Mustela | frenata | Long-tailed Weasel | |
| Spilogale | Western Spotted Skunk | S. putorius | |
| Taxidea | taxus | American Badger | |
| Felidae Cat Family | |||
| Lynx | rufus | Bobcat | |
| Puma | concolor | Mountain Lion | Felis c. |
| Cervidae Deer Family | |||
| Odocoileus | hemionus | Mule Deer | |
| Bovidae Cattle, Sheep and Goat Family | |||
| Ovis | canadensis | Bighorn Sheep | |