These species have been recorded from the Lodge or the nearby Tandayapa Valley. Most of the smaller mammals were identified by a team from Abilene Christian University and Pontificia Universidad Católica del Ecuador.
| White-eared Opossum | Didelphis albiventris |
| Southern Opossum | Didelphis marsupialis |
| Andean Slender Mouse Opossum | Marmosops impavidus |
| Nine-banded Armadillo | Dasypus novemcinctus |
| Ecuadorian Small-eared Shrew | Cryptotis equatoris |
| Tailed Tailless Bat | Anoura caudifer |
| Geoffroy's Tailless Bat | Anoura geoffroyi |
| Chestnut Short-tailed Bat | Carollia castanea |
| Vampire Bat | Desmodus rotundus |
| Little Big-eared Bat | Micronycteris megalotis |
| Thomas's Broad-nosed Bat | Platyrrhinus dorsalis |
| Bidentate Yellow-shouldered Bat | Sturnira bidens |
| Hairy Yellow-shouldered Bat | Sturnira erythromos |
| Highland Yellow-shouldered Bat | Sturnira ludovici |
| Little Yellow-eared Bat | Vampyressa pusilla |
| Hairy-legged Myotis | Myotis keaysi |
| Black Myotis | Myotis nigricans |
| White-faced Capuchin | Cebus capucinus |
| Little Spotted Cat | Leopardus tigrinus |
| Puma | Puma concolor |
| Tayra | Eira barbara |
| Long-tailed Weasel | Mustela frenata |
| Olingo | Bassaricyon gabbii |
| Kinkajou | Potos flavus |
| Spectacled Bear | Tremarctos ornatus |
| Collared Peccary | Pecari tajacu |
| Western Dwarf Squirrel | Microsciurus mimulus |
| Red-tailed Squirrel | Sciurus granatensis |
| Forest Small Rice Rat | Microryzomys minutus |
| Mountane Fish-eating Rat | Neusticomys monticolus |
| Tomes's Rice Rat | Oryzomys albigularis |
