| Neotoma desertorum Merriam, 1894 |
| Neotoma desertorum subsp. grandis Elliot, 1904 |
| Neotoma desertorum subsp. sola Merriam, 1894 |
| Neotoma devia Goldman, 1927 |
| Neotoma distincta Bangs, 1903 |
| Neotoma ferruginea Tomes, 1862 |
| Neotoma ferruginea subsp. chamula Goldman, 1909 |
| Neotoma ferruginea subsp. griseoventer Dalquest, 1951 |
| Neotoma ferruginea subsp. isthmica Goldman, 1904 |
| Neotoma ferruginea subsp. ochracea Goldman, 1905 |
| Neotoma ferruginea subsp. picta Goldman, 1904 |
| Neotoma ferruginea subsp. tenuicauda Merriam, 1892 |
| Neotoma fulviventer Merriam, 1894 |
| Neotoma goldmani Merriam, 1903 |
| Neotoma insularis Townsend, 1912 |
| Neotoma intermedia Rhoads, 1894 |
| Neotoma intermedia subsp. albigula Hartley, 1894 |
| Neotoma intermedia subsp. angusticeps Merriam, 1894 |
| Neotoma intermedia subsp. arenacea Goldman, 1910 |
| Neotoma intermedia subsp. durangae J. A. Allen, 1903 |