Fishes:
- Alligator gar (Atractosteus spatula, almost all Indonesian zoos and aquaria)
- Florida gar (Lepisosteus platyrhincus, almost all Indonesian zoos and aquaria)
- Spotted gar (Lepisosteus oculatus, Dunia Air Tawar)
- Longnose gar (Lepisosteus osseus, privately owned)
- American paddlefish (Polyodon spathula, formerly in Dunia Air Tawar and Jakarta Aquarium)
- Sterlet (Acipenser ruthenus, Jakarta Aquarium and formerly in Dunia Air Tawar)
- Russian sturgeon (Acipenser gueldenstaedtii, privately owned)
- Atlantic tarpon (Megalops atlanticus, privately owned)
- Northern pike (Esox lucius, formerly in Dunia Air Tawar)
- Common carp (Cyprinus carpio, almost all Indonesian zoos and aquaria)
- Common shiner (Luxilus cornutus, privately owned)
- Largemouth bass (Micropterus salmoides, privately owned)
- Longear sunfish (Lepomis megalotis, privately owned)
- Bluegill (Lepomis macrochirus, privately owned)
- Texas cichlid (Herichthys cyanoguttatus, formerly in Dunia Air Tawar)
- Wels catfish (Silurus glanis, formerly in Dunia Air Tawar)
- Bull shark (Carcharhinus leucas, formerly in SeaWorld Ancol)
- Axolotl (Ambystoma mexicanum, Dunia Air Tawar and Jakarta Aquarium)
- Tiger salamander (Ambystoma tigrinum, Museum Komodo and formerly in Dunia Air Tawar)
- Greater siren (Siren lacertina, Gembira Loka Zoo)
- American bullfrog (Lithobates catesbeianus, Dunia Air Tawar)
- Red-eared slider (Trachemys scripta elegans, almost all Indonesian zoos and aquaria)
- Yellow-bellied slider (Trachemys scripta scripta, Lembang Park & Zoo)
- Diamondback terrapin (Malaclemys terrapin, formerly in Jakarta Aquarium)
- Alligator snapping turtle (Macrochelys temmincki, almost all Indonesian zoos and aquaria)
- Common snapping turtle (Chelydra serpentina, formerly in Museum Komodo)
- Razor-backed musk turtle (Sternotherus carinatus, privately owned)
- Common musk turtle (Sternotherus odoratus, privately owned)
- Mexican musk turtle (Staurotypus triporcatus, privately owned)
- Mississippi map turtle (Graptemys pseudogeographica kohni, privately owned)
- Balkan terrapin (Mauremys rivulata, privately owned)
- Hermann's tortoise (Testudo hermanni, privately owned)
- Greek tortoise (Testudo graeca, privately owned)
- Green iguana (Iguana iguana, almost all Indonesian zoos and aquaria)
- Gila monster (Heloderma suspectum, Rimba Reptile Park)
- Mexican beaded lizard (Heloderma horridum, privately owned)
- Corn snake (Pantherophis guttatus, almost all Indonesian zoos and aquaria)
- Milk snake (Lampropeltis triangulum, Taman Safari Cisarua)
- California kingsnake (Lampropeltis getula californiae, Taman Safari Cisarua)
- American alligator (Alligator mississippiensis, privately owned)
- Mexican redknee tarantula (Brachypelma hamorii, Jakarta Aquarium and Dunia Serangga)
- Florida bark scorpion (Centruroides gracilis, privately owned)
- European lobster (Homarus gammarus, formerly in SeaWorld Ancol)
- Red king crab (Paralithodes camtschaticus, privately owned)
- Dungeness crab (Metacarcinus magister, privately owned)
- Giant pacific octopus (Enteroctopus dofleini, formerly in Jakarta Aquarium and SeaWorld Ancol)
- Pacific geoduck (Panopea generosa, privately owned)
- Quahog (Mercenaria mercenaria, privately owned)
- Tadpole shrimp (Triops longicaudatus, privately owned)
- Bald eagle (Haliaeetus leucocephalus, Taman Safari Cisarua and Eco Green Park)
- Golden eagle (Aquila chrysaetos, privately owned)
- Redtail hawk (Buteo jamaicensis, privately owned)
- Peregrine falcon (Falco peregrinus, Faunaland Ancol)
- Mute swan (Cygnus olor, almost all Indonesian zoos and aquaria)
- Wood duck (Aix sponsa, Batu Secret Zoo)
- Rock dove (Columba livia, almost all Indonesian zoos and aquaria)
- Ring-necked pheasant (Phasianus colchicus, Siantar Zoo)
- Cougar (Puma concolor, Taman Safari Cisarua, Batu Secret Zoo and soon in Lembang Park & Zoo)
- Eurasian lynx (Lynx lynx, soon in Faunaland Ancol)
- Eurasian brown bear (Ursus arctos arctos, Taman Safari Cisarua)
- Grizzly bear (Ursus arctos horribilis, Batu Secret Zoo)
- American black bear (Ursus americanus, Ragunan Zoo)
- Polar bear (Ursus maritimus, formerly in Taman Safari Cisarua)
- Eastern timber wolf (Canis lupus lycaon, privately owned)
- Eurasian wolf (Canis lupus lupus, privately owned)
- Raccoon (Procyon lotor, Batu Secret Zoo, Maharani Zoo and Ragunan Zoo)
- American mink (Neovison vison, privately owned)
- European polecat (Mustela putorius, privately owned)
- American beaver (Castor canadensis, Taman Safari Prigen and formerly Batu Secret Zoo)
- Black-tailed prairie dog (Cynomys ludovicianus, Lembang Zoo & Park and formerly Batu Secret Zoo)
- European hamster (Cricetus cricetus, privately owned)
- Fallow deer (Dama dama, Lembang Park & Zoo)
- American elk (Cervus canadensis, Taman Safari Prigen)
- Wisent (Bison bonasus, Taman Safari Cisarua)
- Plains bison (Bison bison bison, Surabaya Zoo)
- California sea lion (Zalophus californianus, Taman Safari Cisarua and Prigen)
- Harbor seal (Phoca vitulina, Taman Safari Cisarua and Prigen)
- Beluga whale (Delphinapterus leucas, formerly in Ocean Dream Samudera)
- False killer whale (Pseudorca crassidens, formerly in Ocean Dream Samudera)