| Taxon | Common Name | Range | Archaeological Occurrence | LAGOMORPHS |
| Lepus californicus | black-tailed jackrabbit | W, C, E | common |
| Sylvilagus audubonii | Audubon's cottontail | W, C, E | common |
| Sylvilagus bachmani | brush rabbit | W, C, E | common | RODENTS |
| Amnospermophilus leucurus | antelope ground squirrel | E | |
| Dipodomys agilis | Pacific kangaroo rat | W, C | genus occasional |
| Dipodomys deserti | desert kangaroo rat | E | |
| Dipodomys merriami | Merriam's kangaroo rat | C, E | genus occasional |
| Dipodomys stephensi | Stephens' kangaroo rat | W, C | genus occasional |
| Microtus californicus | California vole | W, C, E | occasional |
| Neotoma albigula | white-throated wood rat | E | |
| Neotoma fuscipes | dusky-footed woodrat | W, C, E | genus common |
| Neotoma lepida | desert wood rat | W, C, E | genus common |
| Onychomys torridus | southern grasshopper mouse | W, C, E | |
| Perognathus baileyi | Bailey's pocket mouse | E | -- |
| Perognathus californicus | California pocket mouse | W, C | genus occasional |
| Perognathus fallax | San Diego pocket mouse | W, C, E | genus occasional |
| Perognathus formosus | long-tailed pocket mouse | E | -- |
| Perognathus longimembris | little pocket mouse | W, C, E | genus occasional |
| Perognathus pencillatus | desert pocket mouse | E | -- |
| Perognathus spinatus | spiny pocket mouse | C, E | -- |
| Peromyscus boylii | brush mouse | W, C, E | |
| Peromyscus californicus | parasitic mouse | W, C | occasional |
| Peromyscus crinitus | cañon mouse | E | |
| Peromyscus eremicus | cactus mouse | W, C, E | |
| Peromyscus maniculatus | deer mouse | W, C, E | |
| Peromyscus truei | piñon mouse | C | |
| Reithrodontomys megalotis | harvest mouse | W, C, E | |
| Sciurus griseus | western gray squirrel | W, C | |
| Spermophilus beecheyi | California ground squirrel | W, C, E | common |
| Spermophilus tereticaudus | round-tailed ground squirrel | E | |
| Tamias merriami | Merriam's chipmunk | E | |
| Tamias obscurus | chaparral chipmunk | C | |
| Thomomys bottae | Botta's pocket gopher | W, C, E | common | SHREWS and MOLES |
| Notiosorex crawfordi | desert shrew | W, C, E | -- |
| Sorex ornatus | ornate shrew | W, C | -- |
| Scapanus latimanus | broad-footed mole | W, C, E | -- | BATS |
| Antrozous pallidus | pallid bat | W, C, E | -- |
| Choeronycteris mexicana | hog-nosed bat | W, C, E | -- |
| Eptesicus fuscus | big brown bat | W, C, E | -- |
| Euderma maculatum | spotted bat | W, C, E | -- |
| Eumops perotis | western mastiff bat | W, C, E | -- |
| Lasiurus borealis | red bat | W, C, E | -- |
| Lasiurus cinereus | hoary bat | W, C, E | -- |
| Lasiurus ega | western yellow bat | E | -- |
| Macrotus californicus | California leaf-nosed bat | W, C, E | -- |
| Myotis californicus | California bat | W, C, E | -- |
| Myotis evotis | long-eared bat | W, C, E | -- |
| Myotis leibii | small-footed bat | W, C, E | -- |
| Myotis lucifugus | little brown bat | W, C, E | -- |
| Myotis thysandodes | fringed bat | W, C, E | -- |
| Myotis volans | long-legged bat | W, C, E | -- |
| Myotis yumanensis | Yuma bat | W, C, E | -- |
| Nyctinomops femorosaccus | pocketed free-tailed bat | W, C, E | -- |
| Pipistrellus hesperus | western pipistrelle | W, C, E | -- |
| Plecotus townsendii | Townsend's long-eared bat | W, C, E | -- |
| Tadarida brasiliensis | guano bat | W, C, E | -- |