| Neotoma intermedia subsp. gilva Rhoads, 1894 |
| Neotoma intermedia subsp. melanura Merriam, 1894 |
| Neotoma intermedia subsp. notia E. W. Nelson & Goldman, 1931 |
| Neotoma intermedia subsp. perpallida Goldman, 1909 |
| Neotoma intermedia subsp. pretiosa Goldman, 1909 |
| Neotoma intermedia subsp. ravida E. W. Nelson & Goldman, 1931 |
| Neotoma intermedia subsp. vicina Goldman, 1909 |
| Neotoma isthmica Goldman, 1904 |
| Neotoma latifrons Merriam, 1894 |
| Neotoma lepida Thomas, 1893 |
| Neotoma lepida subsp. abbreviata Goldman, 1909 |
| Neotoma lepida subsp. arenacea J. A. Allen, 1898 |
| Neotoma lepida subsp. aridicola Huey, 1957 |
| Neotoma lepida subsp. aureotunicata Huey, 1937 |
| Neotoma lepida subsp. bensoni Blossom, 1935 |
| Neotoma lepida subsp. egressa Orr, 1934 |
| Neotoma lepida subsp. felipensis Elliot, 1903 |
| Neotoma lepida subsp. gilva Rhoads, 1894 |
| Neotoma lepida subsp. insularis Townsend, 1912 |
| Neotoma lepida subsp. intermedia Rhoads, 1894 |