Reptiles

Yellow-headed collared lizard
Speckled earless lizard
Great Basin sagebrush lizard
Northern plateau lizard
Northern tree lizard
Northern side-blotched lizard
Mountain short-horned lizard
Plateau whiptail lizard
Two-lined skink
Wandering garter snake
Desert striped whipsnake
Western smooth green snake
Great Basin gopher snake
New Mexico milk snake
Mesa Verde night snake
Prairie (Western) rattlesnake (possibly other subspecies as well)

Amphibians

Utah tiger salamander (nearly extirpated)
Rocky Mountain (Woodhouse’s) toad
Red-spotted toad
Hammond’s spadefoot toad (possibly in Mancos Canyon)
Northern leopard frog (extirpated from park)
Boreal chorus frog

Fish

Colorado pikeminnow (Endangered, extirpated, not reintroduced)
Razorback sucker (Endangered, extirpated, not reintroduced)
Flannelmouth sucker (nearly extirpated, supplemental reintroduction)
Bluehead sucker (nearly extirpated, supplemental reintroduction)
Roundtail chub (extirpated and reintroduced)
Speckled dace Mottled sculpin (not confirmed, single brief visual record in river bed)
Green sunfish (exotic, invasive)
Fathead minnow (exotic, invasive)
Rainbow trout (exotic, not persistent)